Hmm.. I might have to try to scan a windoze comp for viruses later this afternoon. So thinking the best way to clean up the thing would be doing it from a linux boot and then scan it. First thing to pop up in my mind was "Hey, use the fedora usb drive you've got". So went scouring google for pointers on how best to use clamav under fedora and found one at: http://blogs.warwick.ac.uk/jrose/entry/using_clamav_in/.
Anyhow, to summarise it you have to install the clamav and clamav-update package. Edit /etc/freshclam.conf file. Comment the `Example` line and change the `db.XY.clamav.net` to `db.MY.clamav.net` or whatever your country code happens to be. Run `freshclam` (as root) to update the database and `clamscan -r --quiet /to/windows/partition/mount` to scan the windows mount. The --quite part is so that it'd list only those that have been found problematic so that you don't have to look for them with you bare naked eyes in the middle of thousands of lines of filenames. That should be it. Hope it works this afternoon.