If you have a virus first try to get rid of it. There is no such thing as a non-removable virus - it just depends on how good AND how tenacous you are.
If you really want to go that far (1)Boot with a floppy:
(a) created
before the infection
(b) created from another computer, known
not to be infected with any viruses
and make sure you
write-protect the floppy (very important), or boot from a CD. FDISK the drive & wipe
all partitions, reboot, FDISK & create new partitions, reboot, format with DOS, install.
If you don't remove all partitions and rebuild (or hex-edit the boot sector by hand

) any boot sector viruses will still be there. It'll all be for naught. Your mileage may vary...