Self-explanatory? Depends on your perspective, I suppose - however, re-installing Windows is simple enough...
You don't say what version of Windows you have, so I'm assuming it's XP or Vista. So, disconnect from the Internet and then do this:
1) Put the Windows CD in the optical drive and reboot - the machine should boot from the CD.
2) Assuming it does, it should begin the installation process. After asking you some very basic questions, it will then ask you where you want to install Windows, and will present you with a list of possible places.
3) This list should include the location of your existing installation of Windows. Since you want to completely trash and rebuild the machine, you now need to delete the existing installation. How you do that will depend slightly on the version of Windows, but it should be obvious enough.
4) Once you've deleted the existing installation, tell the setup that you want to install Windows on the blank partition.
5) Thereafter, follow the instructions.
6) Once you've reinstalled Windows, you may need to use the other (driver) CD. Go into Control Panel \ System \ Device Manager and look for any devices which are not set up correctly - this will be shown as a yellow triangle with an exclamation mark in it.
7) Right-click any such devices and select Update or Update driver software. When prompted where to find the drivers, put the driver CD into the optical drive and select it.
8) Install your anti-malare software.
9) Reconnect to the Internet and do a complete Windows update.
10) Update your anti-malware software