Virus in boot sector C:

Hi all. My computer has an unknown virus in the boot sector C: I know that normal antivirus will not get rid of this but I am unsure how to go about ridding my computer of it. Today I tried reinstalling Windows from my System restoration disks, but that hasn't helped. I can't reinstall any antivirus programs either because I am getting error messages. What can I do? Can I use my system restoration disks to just completely reformat or won't that work? Please help, this is driving me CRAZY!

Windows 98 SE
127 MB of RAM

Thanks so much