Well, if you format your system drive while running Windows.. uh.. Windows will stop you, because it can't delete itself. If you mean another drive or partition, yeah. Formatting wipes everything clean.
If you want to format the system drive, it depends:
If you're using Win 98, go to the full MS-DOS mode and type in "format c:"
If you're using 2000 or XP, insert the installation disk, and while choosing a partition to install the system, choose "format partition with NTFS...".