1. Don’t delete files without knowing what you are deleting: If you are in doubt, simply move the file to a different directory or rename it. Then, if you restart your system (or the program) and find out you made a mistake, you can always move the file back or restore its original name.
2. Make periodic backups of your system: If you’re getting ready to do a huge cleaning session, you might want to make a backup right before you start. If you want to rely on an older backup, you might want to have it close by, in case you need it when you start your cleaning session.
3. Be careful how you delete programs: When you install a program, the installation program can move pieces and parts all over the place. When you run the program, it can move more of itself to still other places. Because of that, the best way to delete a program is to use either the uninstaller provided with the software or the Add/Remove Programs applet in the Control Panel. Don’t just delete the main folder for the program. Pieces and parts will remain scattered in all the places.
4. Know what you are doing with the Registry: The Registry is a largely incomprehensible place. Be careful when you are changing or deleting things in the Registry. In fact, make a backup of the Registry before you do any big changes, or simply export a data key when you are getting ready to make more minor changes. Windows does not have a Recycle Bin for the Registry. If you delete something by mistake, you will be glad you made a copy ahead of time.
5. If a new icon shows up on your desktop one day, don’t double-click it: If you don’t know why it’s there, or some program has possibly deposited it there. If you don’t know what it does, why double-click it and run it? A safer course of action is to right-click the icon, choose Properties, and then examine what programs the icon runs.
6. Keep your original program discs accessible: If you change the a program’s installation, you probably need the discs. If you delete a part of the program you shouldn’t, you probably need the discs. If you want to reinstall the program, you probably need the discs. Just keep them close.
7. Use only programs from reputable sources: If you download and run a program from a disreputable source, you could possibly infect your system with a virus or do some other systemcrashing function. So take care while downloading stuff for your computer. Make sure the source and programs and source are reliable.

As you’re cleaning your system, keep a notepad and pen nearby. Jot down each cleaning step you take, along with any oddities you observe. This could be helpful if you later need to track down a problem that crops up.