Talking to a smart guy may seem intimidating at first, but it is just like talking to anyone else. You can use the same techniques to talk to a smart guy as you would to talk to any person you've just met on the street or at a party. As long as you act confident and are interested (or act like you are interested) in what they have to say, there's nothing to worry about.
Ask questions. Most people like to talk about themselves. Smart guys are no different. Ask where he grew up, whether he has any siblings, what books he likes to read, if he's seen any good movies lately. If he's interested in you, he'll ask you some of the same questions and you'll find out if you have anything in common.
Compliment him. Tell him some of the things you like about him.
Tease him a little bit about something small. Don't pick a flaw he is obviously self-conscious about. Tease him about being smart.
Try telling him a dumb, science joke. A good example of one is, "Why did all the ladies love the mushroom? Because he was a real fungi."
If he tells you a joke, laugh.
Be straightforward. Super smart guys can sometimes be clueless when it comes to social situations. If you're interested in him, ask for his number or give him yours and tell him that you'd like to go out with him some time.