When I picked out this girl for a room mate I didn't know she was going to go naked so much?

I'm guessing you're asking what you could do to persuade her to wear clothes in your presence. Just explain that her being around you naked makes you feel uncomfortable, and ask her to remain dressed in the communal areas of your dorm room/apartment. If she finds this to be that unreasonable, perhaps you should consider another roommate.

some people are comfortable with their bodies

Next time she is naked tell her it makes you hard every time you see her (if true) and you need release

Proceed to take off your shorts and sit on the couch. Then see wht happens.

If she doesn't make you hard ask her to cover up

Your apartment too, if you are uncomfortable with it, tell her to keep naked to her room and wear a robe in common areas.

And your problem is.....? Geez, most guys would love to have a female roommate who doesn't mind showing her body off. Maybe she's "trolling" you to try and get some positive reaction from you to take her and screw her, I don't know. Some girls have little shame about their bodies and are pretty open about it. Don't knock it unless it's causing other problems.

If she were my roommate she could go naked as often as she wants.

I don't see a problem. Since she does it does that mean there would be a problem if you did it?