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If you're very uncomfortable in your own living situation, you owe it to yourself to say something in a friendly way. Just tell him how it makes you feel and that you deserve to be comfortable.

With that in mind, he deserves to be comfortable too - and obviously his nakedness and ability to do what he wants makes him comfy as all hell. Time to find a happy medium. Perhaps work with him and see if you guys can work out a schedule. Maybe he gets his naked time, but it's when he knows you won't be around. Post your detailed schedule, and ask if he could try to only masturbate when he knows he'll be alone. Keep in contact and communicate to avoid the awkwardness it's causing you.

If he's adamant that he wants to be able to be naked in his residence whenever he wants you have two options - you deal with it and try to ignore it as much as possible, or if it bothers you too much you find a way out.

Other option? Get naked too and join the party!

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thats the best answer given...especially about the part of joining him, haha.   but hell, why not.

If I had a roommate like your I would have to assume he's making himself available for sex.  I understand why it's making you uncomfortable.