It'd still be there so I'd be careful. Personally, I wouldn't want to bother with trying to remove a virus that's hard to remove and wreaking havok so I'd just back up what I need and reformat the hard drive. Regardless of what you choose to do, I'd make sure that before you access whatever it was that you backed up, scan the flash drive (or whatever) that you copies the files to with an updated anti-virus first.
If you want to play it safe you can download the latest version of Ubuntu, burn it to a disk, and boot to the disk and run the live CD. It'll load Ubuntu without installing it and you'll be able to access your hard drives and grab any files you need to backup and copy them over to a flash drive or something.
http://www.ubuntu.com/getubuntu/download
