Your title suggests that these two drives are USB drives, but your question suggests that they (or, at least, one of them) may be your boot drive. Could you explain in more detail what you meant by USB?
If these are not your boot drive(s) and you're running as SU, just umount the partition(s) before using the partition editor.
It they are your boot drives, try starting the partition editor and then (e.g, by pressing Ctrl-Alt-F1) start another terminal session where you can umount the partition(s). If the partition editor has been loaded into memory (and/or swap), you should be able to finish the formatting. Of course, formatting your boot drive(s) will erase you system, so I wouldn't recommend it.
Also, if you are happy with the partitioning, use the mkfs command to do the formatting.
Last edited by PTrenholme; 09-28-2007 at 04:08 PM.