If you're formatting, you obviously plan on reinstalling the operating system. If your computer boots off CD-ROM, then all you have to do is issue the format command. If not, you'll need to make a boot disk (Windows calls it a "start up disk") There's a tab in the My Computer properties for that.
After the boot disk is made, write protect it and boot off it. Issue the command "Format c: /s" at the dos prompt and let it go. If you don't make a boot disk, use the start up menu (Press F8 when the "Starting Windows 98..." dialogue appears, I think) and select "Command Prompt Only." Then, issue the "format c: /s" command.
When it's done, you may want to power down your machine (not a requirement, but a suggestion to prevent possible problems) and reinstall your OS.