If you format, and copy everything from a CD or download it from the internet, how can you copy it then?
Hackers can alter existing files, mostly they alter system files, those you won't delete that fast and are used very often. They can also just alter any file they want with virus that than would copy a tojan back into you system files. Safest thing to do is not to install any bakups back untill you know you've secured your pc as much possible.
