You can use either an MS-DOS bootable disk (making sure your floppy drive is first in your boot sequence), or press (I believe) F4 sometime during the start-up and should recieve a menu to select MS-DOS from. From there, as stated in a previous response, type format c: and that should do the trick.
You can also clear your partitions by running most OS installers, which of course you do outside of Windows by setting your CD/floppy drive as the primary boot device and then placing the media in the drive and rebooting.
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windows will not let you boot into dos. Atleast not 2000. There is no option. It lets you boot from 'safe mode with command prompt'. You also do not need to boot into dos to format your drive. Just do it with whatever you are installing, every windows install cd, and every linux install cd will be able to format your drives and setup your partitions. You booting into dos to do it is extra work.