Basically you backup anything you want to keep. Files, documents, pictures, music, game saves, whatever to another drive. When you do a clean install you have to format your drive otherwise it's pointless because it isn't "clean". You have to reinstall your games and programs.
After you are done backing up it is as simple as sticking your Windows DVD in (or if you want to make a flash drive you can), boot to the DVD or flash drive, click the install button, accept EULA, click custom advanced install, delete partition on the drive you want to install Windows on (obviously not the one you backed up to, actually I recommend unplugging that one), create partition and click yes when it asks about a system partition, click on the bigger partition (primary) and click install. Sit back and let it do its thing, then when you are finally in Windows install drivers, your programs, and continue as normal.