Backup data if any (any backup could be infected), run fdisk from the floppy (it could be infected if not write protected--tab in the corner of the floppy), and remove all partitions (destroys all data, etc.). Delete logical drives first, extended partitions second, and the primary partition last. Reboot so it will take affect.
a:\> fidsk /mbr
… to write-out a new Master Boot Record to the hard disk drive and rid the drive of many, but not all, lingering virus code (something that should be used with data on the drive only as a last resort). Reboot. Better yet… there are programs out there that can be used to write 0’s, etc. to the drive (e.g., http://download.cnet.com/downloads/1,10150,0-10001-103-0-1-7,00.html?tag=srch&qt=wipe+disk&cn=&ca=10001). If you have a Western Digital drive, WD DIAG (http://duxcw.com/digest/Fromshop/diags/wddiag.htm ) in WD’s Data Lifeguard tools will do it.
Create new partitions, reboot, and format (http://duxcw.com/digest/Howto/software/windows/upgrade/fdisk.htm). Do not transfer system files. Run another virus scan to check the boot track.
Some viruses infect the motherboard CMOS memory. You may want to clear the CMOS before proceeding. Most motherboards have a jumper that will do it. Be sure the power cord is pulled before putting, and while the jumper is in the clear position or damage can result. Leave it in the clear position for about 10 minutes or so (varies with motherboards).