1. First back up all your important data on to a separate partition/hard drive (emails docs etc)
2. Do a clean install of your OS from the install cd
3. Disable any computer virus programs ( this is controversial but all virus software by definition only works for known computer virus so you are no safer from a threat then if you did not have it. Providing your system is clean of course)
4. Install any other software needed, Printer drivers, Photoshop etc
5. Test it for a couple days and make sure you are happy
6. Make a ghost image or copy of this partition using any of the following software, partition magic, Norton ghost, Acronis, shareware etc
7. Use your computer…
What you will have created is a system that allows you at any given moment to return your computer to its optimal state from the restore. So long as your files are kept safe on a separate hard drive or partition and you make a regular backup you should be fine.