Well, you see:
If you want to protect your data, all your data will have to go...
A shredder program takes a file. This isnt how it really works, but lets say the file has this data in it:
The quick brown fox jumps over the lazy dog
Then it takes that data, and turns it into something else, like this:
00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx00xx
Then it takes it again, and turns it into:
23049ei0fk02mrf3iteb093qnignvie39t0q49jgvm34wq-qt0jf4i3n3thbpodfng93m5e4rhtbipon3903qng
And then, it deletes the file. When you delete a file, it is still there, its just hidden. A shredder program makes sure that even the deleted data is still unreadable, even by an expert.
Thus, rendering your computer cleaned.
Now, as for deleted software, as long as you dont have the discs, you wont be able to get it back to brand new conditions. You can call the manufacture of your computer, and they may be able to send you a new disc, however, point of the matter still remains, even with that disc, your personal data will continue to exist in the background of your data... you will need to use a software data shredder, or replace the drive.
What kind of computer are we talking about here, is this something capable of the Internet? What OS did it have installed on it?