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Give Windows a Clean Start - How To Reinstall Your OS the Right Way



Clean start. OS reset. Nuke and pave. Whatever you call it, no matter how good a personal system administrator you are, there’s a time to take your OS install out behind the shed and put two in its head.

When would you need to take such extreme measures? If the networking stack is splayed out on the floor and no amount of patching, registry editing, or Winsock repair tools can fix it. If you can’t get hibernate or standby to work anymore. Or if you’ve had a horrible malware or rootkit breakout. Sure, you may have reclaimed control of your PC after an epic five-day battle with the beast, but can you really trust your OS anymore? You don’t want to reenact the final sequence from The Thing, you and your PC eyeing one another wondering if the other is not what he seems to be.

A clean start is the only way to relieve your paranoia. It can also save you countless hours of troubleshooting and tweaking a misbehaving machine. Follow along as we instruct you on the proper way to do a clean install—whether you’re using XP or Vista—that will have your OS acting like the young pup it once was. Plus, we’ll show you how to create a pristine image of your OS that’ll save your bacon the next time your rig melts down.   

Out With The Old, In With The New

Before embarking on our clean start regimen, read through the instructions to make sure you have all the tools you’ll need and a thorough understanding of the process.

Buy Some Breathing Room

screen shot of app Magical Jelly Bean Keyfinder
Magic Jelly Bean 2.0 may help you locate serial numbers you’ll need to reinstall your applications.

You can do a clean start using just your old drive and a pile of DVDs for backup, but we recommend that you use our method and buy two new hard drives. You’ll use one as your new C: drive and the second to store your backups and images. (Consider the original drive as a backup of all your data up to this point.) Here’s our reasoning: First, an OS reinstall is the perfect time to make the jump to a new drive. Second, the performance benefits of your clean install will only be enhanced by using a newer, larger drive. The new 1.5TB Seagate Barracuda, for example, has an average read speed of 104MB/s. Your old 500GB drive probably tops out in the 50MB/s to 60MB/s range, depending on the generation of the drive.

You’ll also see significant performance benefits if you have a lot of data because a drive’s performance weakens as it approaches full capacity—so that 400GB of data on a 1.5TB drive or even a 1TB drive won’t impinge performance as it would on a 500GB drive. Finally, storage has become one of the most inexpensive components in a PC. So take our advice and spend the $200 on two new 1TB drives and save yourself some heartache.

If you choose to ignore our advice and reinstall the OS on your original drive, you must back up all your data to discs before proceeding. 

Take Stock of Your Apps

Before you make a clean start, you need to consider the applications you’ll be bringing with you. First, make sure you have all of your application discs. One of the most important tasks is to take stock of any registration codes that you need for your software. Locate and record the registration keys that you will need. If you can’t find the keys, try Magic Jelly Bean 2.0, a free utility available at or The application will search through the registry for application keys. It won’t find all the keys you need, but it might help you locate that one key you can’t find.

Magic Jelly Bean 2.0 is sometimes identified as a hacking tool by antivirus apps, but if you download it from a reputable site such as, you should be fine. If you can’t locate a particular key, contact the vendor for a replacement key or a copy of your original key before you proceed if you know you’re going to need access to the app. You did write down your Windows XP or Windows Vista key, right?

Deactivate Your Apps

screen shot of deactivation message for CS3
It’s very important that you deactivate some applications, such as Adobe’s Photoshop CS3, before you take down your old drive or you may have problems reinstalling it.

Many applications require activation before running—even if you have a legitimate serial number. You can’t, for example, reinstall Photoshop without reactivating it, so deactivate any programs on your old drive that use this copy-protection technique.

Software activation is the harsh consequence of software piracy. Fortunately, it’s merely an inconvenience, not a major undertaking. To minimize your reinstall efforts, you should take stock of the applications that require activation before you do your clean start. Most professional Adobe applications require that you deactivate the program before it can be installed elsewhere. To do this, click Help and then Deactivate. This should deactivate the suite, but to be safe, fire up your other Adobe apps and check to see if they have been deactivated.

You’ll need Internet access for the application to talk to Adobe’s servers. Adobe’s activation is more finicky than the one Microsoft uses, and disk changes, such as imaging from one drive to another, can trigger activation. For other programs, you may want to research how the individual software vendor treats reactivation. Microsoft Office 2007 can simply be reinstalled on your new hard drive and reactivated. You’ll likely have to reactivate by phone though, as the program may fail an Internet reactivation. Just explain that you are installing to a new hard drive and you should be fine.

Not all vendors are as accessible, however, so if there is a critical application that you need access to, you may want to contact the vendor first to find out what the activation policy is. Obviously, if you don’t know if the program will reactivate and you need to access it, wait until you have the answer before you do your clean start and consider doing your reinstall during normal business hours when the vendor can be contacted.

Prep iTunes and Steam

Moving your iTunes library is fairly easy, but it can be made more complicated by differences among versions. If you’re running iTunes 7 and plan to use iTunes 8 on your clean install, we suggest that you install iTunes 8 on your existing hard drive first. It doesn’t always happen, but people have reported issues migrating the database from iTunes 7 to iTunes 8. You should also consolidate your library by going to File > Library > Consolidate Library in iTunes. This will copy the various music and video files that are scattered around your PC into the iTunes directory at C:\Documents and Settings\your user name\My

Documents\My Music\iTunes (or C:\Users\your user name\Music\iTunes on Vista). Once you’re done, migrating your library is as easy as copying the iTunes folder of your old drive into the \My Documents\My Music\ folder of your new drive. Your final move in iTunes will be to turn out the lights. In iTunes, go to Advanced > Deauthorize and deauthorize the computer. This will prevent you from playing any protected content that you downloaded from iTunes on your PC until you have reauthorized the computer on your new OS install.

screen shot of stream games app
Backing up your Steam games with the app’s built-in utility will save you a lot of downloading later on. Alternatively, you can copy the entire Steam directory over from your old drive to your new one.

Likewise, if you have any games using Valve’s Steam service, we recommend that you use the program’s built-in backup feature to create a backup of your games folder. Generally, just copying the entire Steam directory over to the new install will work, but having the backup file will help should you encounter problems. While the old drive is up and running, you should hunt down any saved games you want. We can’t tell you where to find the saved games for each particular title, as developers use different locations. Check the individual C:\Program Files\game name folders to see if the saved games are there, if they aren’t in a subfolder of Documents.

Collect Your Drivers

Gather all the driver discs for the peripherals connected to your PC. If you can’t find a particular disc, chances are you can get the driver off the manufacturer’s website. There’s no reason to rely on the driver CD that came with your motherboard since it’s likely out of date. Go to your motherboard vendor’s site and download the latest drivers and applications for your board. The NIC driver is most critical. It’s unlikely Windows XP will have native NIC support, so you’ll need the driver. Microsoft Vista could have support for it, but many newer chipset NICs are not supported, so download the version you need. You should also download the most recent drivers for your videocard and any other add-in cards you have in your PC.

While you’re online, download the latest Service Pack for the OS you’re installing. If you have a Windows Vista disc with SP1 already integrated, don’t worry about it. If not, download it here. For Windows XP, you’ll want to download the network installation package of the Service Pack. It’s designed to be installed on multiple computers, but it will also let you install the Service Pack without having to connect to the Internet. You can put all the drivers and the Service Pack in a folder on the hard drive you’ll be replacing or save them to a USB key.

Say Your Goodbyes

screen shot of windowws boot manager
Complain about Vista all you want, but the installation process is exceedingly easy. After launching Setup from the DVD, you can be on the desktop in as few as seven steps.

OK, you’ve got your keys and apps, your drivers and Service Pack. It’s time to leave behind your previous install. Completely power down your machine by unplugging it or switching it off at the PSU. Open your PC and install your new hard drive in an empty bay and plug it into an open SATA port. Remember, some motherboards use multiple hard drive controllers. You should plug your drive into the ports numbered 0 to 3 (for a total of four) as they are usually the SATA ports native to the chipset. If you use a third-party controller chip, you’ll need to have the drivers for it on floppy disc for XP. Vista supports USB and optical devices for drivers, so you can use the CD that came with the mobo or just drop the drivers on a USB key.

Since we’re going to copy the files directly over from the old hard drive to the new one, we recommend that you unplug your old drive’s SATA and power cable for now so you don’t accidentally reinstall Windows over your critical data. Once you’ve done this, boot the machine and put the OS disc in the optical drive. The optical drive is usually first in the boot order, but if it isn’t, go into the BIOS and set it as the first boot device. Some boards let you temporarily alter the boot order by hitting F10, F11, or F12 during boot. If your board doesn’t, you’ll have to go into the BIOS by hitting DEL or F2 during boot and change the boot order so that your optical drive is first. Finally, disconnect your computer from the Internet.

Ready, Steady, Go! 

Let’s start with Vista: Hit the space bar during boot and begin installing Windows. Installing Windows Vista is very straightforward. Just enter Windows Setup, enter your product key, select the version of Windows you bought, and hit Next. Accept the terms of the license and continue until Vista asks you what kind of install you want.

Since the new drive is empty, you’ll be offered the Custom option to install a clean copy of Windows (Upgrade appears only on a drive with an OS on it). After you click Custom (Advanced) you’ll be asked what drive you want to install Windows to. If you’re presented with drive letters you can’t account for (your single, new drive should be a single Disk 0), the OS is likely recognizing a multiformat memory-card reader as multiple hard drives. Vista does not have issues with this, but Windows XP will sometimes install the OS as the F: drive because of a multiformat card reader. Having Windows XP default as anything but C: causes all kinds of problems and we generally don’t recommend it. There is a way to fix it, but it’s not pleasant. If this happens, power down, disconnect your card reader, and restart.

screen shot of window installer
Most people will be suited by using one single contiguous partition for the OS, so just click next and Vista will format the drive that way.

After selecting your hard drive, click Next to continue with a standard single-partition install. For most people, a single partition on the drive is fine. If you like to separate partitions for data and apps, select your main drive and click New. Enter the size of the partition you want, click Apply, and continue on with Next.

If you’re running a RAID configuration in Vista or need to install special drivers for your controller card, hitting Load Driver will allow you to install the drivers from a floppy, CD, or USB key. After you’ve pointed the installer at the correct drive, Vista will scan it and present a list of available driver options. Select the driver you need and click Next. Vista will now install the OS to your drive in 30 to 60 minutes. When you come back to the desktop, you’ll be asked to enter a user name and password. The only decisions you’ll make from this point on are the name of the PC, the desktop background, the Windows update settings (Recommended Settings is right for most people), and the location setting for the Network: for home, select Home, if you’re at work, select Work.

screen shot of windows installer app
Loading third-party drivers for RAID, SCSI, or other controllers is a snap in Vista and you can finally do it from a USB key! 

A RAID config on XP is a different story. If you want to install RAID, AHCI, SCSI, or any third-party controller drivers, they can be installed only from a floppy drive, and many XP discs will not support newer USB floppy drives. Even more inane, to install the drivers, you’ll need to punch the F6 key within a three-second window just after the installer has started. It’s like Dragon’s Lair but without the fun; miss the F6-key window and you’ll have to reboot and try it again until you hit it just right.

screen shot of windows setup
Blink and you may miss the F6 prompt during Windows XP’s install for third-party drivers such as RAID, AHCI, or SCSI.

If you have timed it right, you’ll see a screen that tells you that the OS cannot determine the type of mass storage controller. Put your floppy with the drivers in, hit the S key, and select the device driver you need. XP will continue to ask you if you need to install additional drivers, but if you’re done, just hit the Enter key.

The installer will present you with what drive you want to install the OS on. Unless you need to create multiple partitions, just hit Enter. Windows XP will now give you a choice of a quick format or a full format. The rule of thumb is to do a full format on new drives since the OS will map out any bad sectors on the disc. Quick formats should be done only on drives known to be good. However, a full format on a 1.5TB drive will take hours to run.

screen shot windows XP setup
If you are installing Windows XP on a new disk, we recommend that you perform a full format that maps out the bad sectors on the hard drive. If you skip this, you can perform a chkdsk/r at a later point.

If you don’t like to be told the odds, do a quick format and then perform a chkdsk /r as soon as you have some spare time. Once the format is complete, XP will begin the install. At some inconvenient point, XP will ask you to customize your region settings, enter a user name and password, enter your product key, name the PC, and set the time. You’d think that would be all it needs, but after 20 minutes or so, XP will halt the install and ask you for network settings (select Typical Settings and click Next) and any work group or domain settings (enter these later or just accept the default and move on; you can change these later). Now XP will make you wait another 10 or 15 minutes while it finishes. This stop and go can mostly be avoided by building an automated slipstream disc using nLite, but honestly, unless you install the OS a lot, it’s faster to just deal with the prompts.

Install Service Packs

You disconnected your PC from the network, right? This is just an optional precaution for Vista, as its firewall is on by default. But, it doesn’t hurt to be extra careful, so until you have the latest Service Pack installed, don’t connect your rig to the net. Windows XP is far more vulnerable because non–Service Pack builds don’t have the firewall on and connecting the machine directly to the Internet will infect a new install almost instantly. We know of people who got caught in an infinite loop of getting infected and not knowing how it happened since each instance was a “clean” install from a factory Windows XP disc. Even if you’re on the other side of a router, there’s no guarantee that your PC won’t be infected by a machine inside the network, so disconnect that XP box.

Once the machine is running, power down and plug your old hard drive back in and boot into the BIOS. Make sure your BIOS is set to boot from your new drive, not your old drive. Now boot into the OS. Find the old drive (it will have a letter other than C:) and install the Service Pack you downloaded. For Windows Vista, Service Pack 1 is the current version. For Windows XP, it’s Service Pack 3.

Move In

The first driver you install should be the chipset driver. Next, reboot and install the audio drivers, NIC, SATA, and any other devices your board has. Some of the drivers will require a reboot and should prompt you if they do. Once those are done, move on to your other devices, such as the graphics card, add-in soundcard, and TV tuner. Now connect the machine to the Internet and run Windows Update. You might also need to activate Windows. If Microsoft’s server doesn’t accept the activation, be prepared to do a phone activation. Now, install the applications you gathered up earlier and do any OS tweaks, such as setting the standby mode, installing your favorite screensaver, changing the desktop background, and arranging the icons just so.

Migrate Your Data

Now it’s time to move all your data over to the new drive. Open My Computer, find your old drive and start copying your files over. In Windows Vista, the bulk of your user files are located in C:\Users\your user name. Since your new drive is so deliciously huge, you can copy the contents of the directory over to your desktop. This will let you go through the folders and conduct a spring cleaning to weed out, say, that 10GB of blurry photos. One thing you can instantly do is move your iTunes directory over, after first installing iTunes on the new hard drive.

Windows XP users can find their iTunes folder on the old drive by looking in C: \Documents and Settings\your user name\My Documents\My Music\iTunes; Vista users can look in \Users\your user name\Music\iTunes\. Copy the contents from there to the same place on the new drive.

For Steam games, download the latest version of Steam and install it. In Vista x64, copy over the Steam Apps directory from \Program Files (x86)\Steam\ to the same directory on your clean drive. Relaunch Steam and your games will be ready to play. Windows XP and 32-bit Vista users will find the files in \Program Files\Steam\.

Consider Your Image

Once you have your OS installed, patched, and tweaked just the way you like it, you should make an image of it. A disk image of your pristine OS allows you to instantly have a custom reinstall up and running should you experience a catastrophic malware attack or hard disk failure. We like Acronis True Image Home 2009 ($50,

screen shot of Acronis ture app
Acronis True Image 2009 is fairly easy to use and lets you make complete images and file backups, including specialized backups of email, the registry, and application settings.

If you haven’t used disk imaging software in a while, you’ll notice that it’s changed quite a bit. Disk imaging used to be run only on occasion to create a static image that when used would take your machine back to the very day the image was built. While it would save you the time of dealing with an OS reinstall from scratch, you would have essentially lost months of changes.

screen shot wizard backup
You can set Acronis True Image Home 2009 to make a monthly image of your machine so a restore won’t take you back to day one. You can also tell the program to back up your application data and documents on a daily basis.

Today’s disk imaging applications not only build an initial static image, but also update the image, so you could, say, restore the PC to the state it was two weeks before the drive went kaput. The apps also now support file backups, so you have two layers of safety: first, a full image that is updated on a monthly or biweekly basis. File backups can be done weekly or daily depending on your level of paranoia.

Set up Your Safety Net

You’re no longer at risk of simply losing your old schoolwork when your hard drive craps out. Today, a hard drive failure will wipe out gigabytes of invaluable memories and entertainment. While an external RAID 5 NAS backup drive would provide peace of mind, that’s a silly-expensive solution and rather slow. And even pairing a backup drive with your primary drive in RAID 1 isn’t the best solution. We like to use a single backup drive equal or near-equal in size to our primary drive along with a disk imaging app—in this case, Acronis True Image.

We set the disk imaging app to make a weekly image backup of our primary drive and file backups every other day. We like this configuration because it gives us some fallback that a RAID 1 array doesn’t. If you erase something on RAID 1 and realize you need it the next week, it’s gone. Or if a virus runs amok on your primary drive, it does so simultaneously on its RAID 1 counterpart. With a disk image and regular backups, you can choose from multiple points in time to recover.

So power down your machine, disconnect your old drive, and put it in a safe place. Install the second new drive, plug it into the port the old drive was in, and power up. Right-click My Computer, click Manage, select Storage, and Windows should ask you to initialize the new disk. Create a partition on the drive and format it. Again, unless you have a need for separate partitions, one single contiguous partition mitigates the drive letter confusion.

Schedule Your Backups 

Install True Image Home 2009. (Note: Although Acronis True Image Home 2009 works with RAID, it doesn’t work with all RAID configurations. Acronis’s True Image Echo Workstation is a better choice for RAID imaging, albeit more expensive.) Launch the program, click Back Up, and select My Computer. Select the C: drive for backup. Click Next and select your target for the archive. Choose the second drive, create a new folder by clicking Create New Folder, name the file, and click OK. In the Scheduling pane, select a backup schedule that works for you—one that doesn’t run during the times you use your PC. Enter a user name and password so Acronis can run the backup unattended. Under Backup  Method, select Incremental. Hit Next for the next four tabs and your hard drive will be backed up on the specified schedule.

You should also create a separate image that you keep handy if you do need to roll your machine back to day one status. To do this, go to the opening menu of True Image, select Backup and Restore and My Computer, select your C: drive, and click Next. Select Target archive and put the image in a directory on your second drive. Name the file Day1.tib. Select Schedule and make sure it is set to Do Not Schedule. The window should say “Run this task manually.” Click Summary and then Proceed.

You should also now set True Image to make automatic backups of your data. After you select Backup and Restore, select the My Data option. This will let you select the type of data you want to back up and the frequency of the backups. You can run it daily or every other day since the process should be much faster once you’ve made the initial backup.

And before you finish with Acronis, you should create a boot disk, which, in the event that your drive or OS goes kaput, will allow you to boot the machine in order to access the restore image from your backup drive. Do this by clicking Start > Programs > Acronis True Image Home > Bootable Rescue Media Builder. Select Acronis True Image Home, click Next, and Next again, and select CD-RW. Pop a blank disc in the optical drive and your boot disc will be created.

Congrats. You’re done and fully prepared for just about any type of catastrophe.

Restoration Software

Putting your defensive strategy to work

screen shot of acronis app
Restoring your image is as easy as popping in the boot CD, selecting the image you want to restore, and waiting for your system to come back to life.

So the worst case scenario happens: Your hard drive dies or you try a Windows “performance” trick and accidently nuke everything on your drive. Not a problem. Grab the True Image Home 2009 rescue disc that you made and drop it into the optical drive. Boot the machine off of the disc. Select Acronis True Home 2009 and click Manage and Restore. Locate the image that you want to restore from your secondary hard drive. If you want the last automated image True Image Home made, select that. If you decide you want to go back to your day one image, point it at that directory.

screen shot of acronis app
Make sure that you select the correct disk that you want to restore your image to.

Select Restore Whole Disks and Partitions and then select the disk you want to restore from the backup image. Since you had only one partition on your original drive, you should be presented with only the C: drive and the MBR and Track 0. Select both. Now select the destination drive where you want the partition to go. If the target drive still has a partition on it (whether infected or corrupted) you’ll get a warning message saying so. Just click OK. Click Next until you get to the Summary screen and click Proceed. True Image will proceed with the image restoration and you should be able to boot directly into the OS as it was last backed up.