The avast! virus scanner lets you scan your FAT16/FAT32/NTFS disks for virus/worm/trojan infections and optionally gives you the ability to remove them.

avast! supports scanning inside file archives, giving you the chance to thoroughly check all parts of the disk.

It is also possible to scan only certain folders, if you have a suspicion that the infected files are located there.

Last but not least, it is possible to use an alternative virus definition file that you can supply, e.g., on a floppy disk.