Fdisk and delete all the physical partitions, then assign your partitions again and format - clean as a whistle after that.
I suggest making a boot disk that supports CD-Roms, like a win98se boot disk, then copy the Fdisk program and the Format program onto it from your windows\command directory if they're not already on the floppy. You really want to boot from floppy then wipe the HDD, especially if this is to obliterate any nasty viruses. When partitioning your hard disk, plan it out, decide how much space you want for your system files, 2-3gb is usually plenty. Remember that the smaller the partition, the faster it'll work, so keeping your system partition small is a good idea in terms of performance.
Van-B
My cats breath smells of cat food.