There are all sorts of ways to proofread, and we generally need to use several of them. Try reading your paper out loud, marking the places where you stumble. Run a spell-checker, but don't assume that this tool will catch all of your problems. A spell-checker, after all, will think that the sentence "A cities main urban problem is often it's over crowing" is fine; the spell-checker won't know that you meant to write "A city's main urban problem is often its overcrowding." As you can see, spell-checkers can create new problems, sometimes leading to unintentionally funny moments. Be sure to proofread after spell-checking, as well as before.
In short, proofreading requires several passes at a paper. As with revision, we need to develop new eyes in order to catch our mistakes. We need to become aware of our bad habits. For example, if you know that you have a tendency toward passive rather than active sentence structure, it's a good idea to devote one reading of your paper to looking only for passive construction. We need to train ourselves, through habit, to see the things that are normally invisible to us.