We could use Antivirus and deframentation for DOS(or Linux), like a bootable cd with an interface like the GUI in linux-knoppix, and have it load all partitions or external hard disks as well, NTFS, FAT, FAT16, FAT32, SWAP, NFS, etc Then have it scan those drives without the OS running, you could have an option to save the infected files to floppy, or USB- only if the Drives could be used in the GUI.
Something like a Bootable Linux (Knoppix) (:KWL)(Comodo Linux)(:KWL) but have your software load up from boot… This would allow a complete defragmentation to complete, and allow a full antivirus to run without any interruptions, this would probably stop the viruses from executing in a windows interface as well, considering the cd you also could allow access to NTFS partitions to move or delete files, like a file manager like midnight commander, or possibly like the old DosShell…