I'm not totally sure I understand, but some random suggestions:
In a windows bootdisk, you can use fdisk /mbr to clear the master bootrecord, but it doesn't sound like that's what you want to do.. I think.
Whatever the case, a Linux LiveCD should do the job for you. Boot off Knoppix or whatever and you can edit/format/etc your hard drives until your heart's content.
If you have a linux partition and you want to format it in windows (which is what the subject of this is), and you still have a running windows, you can do it in Disk Manager. If you don't have a running windows, get a Win98SE boot disk and use fdisk from it to delete the linux (non-DOS) partition, recreate it as a normal DOS/Windows partition, reboot, and then format it (using that same boot disk).
www.bootdisk.com is handy.
I hope this helps in some way, still not sure what's going on
