How do I prepare against someone if I have a database of his games ChessTempo offers a service to see all the games of your opponent. The thing is, it also shows what the opponents played. So if I see 100 times e4 was played, 60 of the times might be because of the opponent. How can I only see the moves made by the person I'm going to face?
First of all, I don't think that chesstempo or other sites are actually good for preparation. I just took a look and saw that there are only 9 moves of each game displayed. If you are taking chess seriously, it's better to get the chessbase or at least fritz. They are more user friendly and statistics are better.

Regarding your question's title. Preparation is a complicated process. It depends mostly on time you are willing to spend on it. If you got tons of time and the game you are preparing to is very important, you should totally x-ray your opponent looking at all the games. Probably with someone more experienced in order to advise you a little bit.

Anyway, some basic stuff:


Check what openings your oponent play and what is his win rate/draw rate/lose rate, you know why.
What is your standard answer to his opening? Do you feel comfortable with it? What's your W/D/L ratio there? Are there game of YOURS in database? Keep in mind, your oponent might be prepared aswell! 
Are there any games/variations that your oponent has a big lose rate? How well do you understand those positions? Do you know any similar structures that you could drag him into?


So in simple words: spot the weakness and exploit, that's it.