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Get a nice Ubuntu "live" dvd/cd prefferably the latest version. Ubuntu Ultimate is the best for any purpose. Download and burn on a DVD: http://ultimateedition.info/. Some of the cds/dvds are install only. Thats of no use here.
Boot from the DVD. If it doesn't boot, then check the boot priority in the BIOS. Set it to boot from Optical drive first.
You will end up with an awsome desktop environment. Go to Places > My Computer. You will see your drives there.
Insert your backup drive (pendrive/portable hdd/any other media). Delete all the previous data which includes .vbs/.exe/.js/.bat/.com/.inf etc permanently. In case, they are important, then create a new directory and name as "scanme" and copy all such files there.
Copy data to your backup drive. The my documents and desktop directories will be available here: <%system%> / Users / <%user_name%> / for vista users and <%system%> / Documents and Settings / <%user_name%> / for xp users.
Begin the installation of a fresh copy of Windows. For this, you need to delete all the partitions and create new partition(s). This will ensure that any virus in any of the partitions on the harddisk are wiped away.
After installation, you will have a virus free system. Install all the necessary drivers from a "trusted" source.
Install a good antivirus (Norton/Nod32/Norton360 - preferrably Norton Internet Security 2007 or 2009). If the installation file existed on the infected system and hence in the backup drive, then please don't trust it !!! Its very much likely that the installation file(s) for the antivirus are affected by the same virus.
Scan the system first. Scan the "scanme" folder of your backup drive. Continue using windows.
You can format your new partions which you would have created during installation of OS.
Copy all the important data from the backup drive.
Continue using windows happily. To avoid any further problems you must follow the suggestions here : How to keep your system safe
It is highly recommended to install Ubuntu Ultimate 2.2 on your machine along with Windows. http://ultimateedition.info/