Doesn't F-Prot have an "automatically delete" feature?

I could write and test a script I would be happy with in an hour or so, but, it would be easier to just connect the drive to another windoze box and then do a virus scan from a native ntfs operating system.

Either way, an operating system with "a ton of stuff" is unlikely to be the same after removal if it even boots. Backup any important data and reload.