Since you are obviously wearing clothes when he "scans" you, there is the possibility that he is attracted to your clothes.
Sometimes the answer to "how do I confront him" may actually be: I'd advise you not to be too hasty. Because in some cases (such as misunderstandings or lack of communication), confrontations simply make things worse. You say the guy "scans" you. You assume there is something sexual about that behavior, but don't know for sure, quote: "I'm not 100% sure this is sexualised harassment, but it's very annoying..."
Simply being annoyed with someone you are not even on speaking terms with, isn't reason enough to accuse someone of seriously inappropriate behavior. If you were on speaking terms with your co-worker, you wouldn't be so confused about his motivations. It wouldn't take long to find out whether there was anything to be seriously concerned about. And if you for whatever reason just don't want to talk to him, then you should at least understand that snubbing him probably makes him feel uncomfortable.
And presuming the guilt of someone you apparently don't know very well, if at all, without rational evidence of wrong-doing, is both extremely humiliating for him, and very unwise on your part.
Being unnecessarily confrontational is not very skillful social conduct, and I'm sorry to see that so many answers have encouraged it.
But let's assume for a moment that your intuition is correct: he's a creep. You can accuse people of being creepy, but it doesn't usually go over very well, for all concerned. The best way to handle creeps and stalkers, who are too sneaky to get caught (yet), is to steer clear of them. And since there already is apparently no real communication between you, you only see him occasionally in the break room, and his worse crime is just looking at your clothes -- that shouldn't be too difficult.
UPDATE: (Advice on how to handle the specific situation which is uncomfortable for you.)
The next moment you are certain that he is "scanning your body", immediately turn to him, making direct eye contact (if he doesn't make eye contact, you may briefly point your finger, to get his attention), and say:
"Listen here, I want you to stop staring at my body."
If he denies it, say, "Just stop it. I'm not going to tolerate it anymore. No more discussion, no excuses. I see what you've been doing; it's been going on for far too long now, and I've had enough. I'm not going to put up with it."
You should be perfectly calm, not scared or angry (remember, you said he is "usually nice"); but absolutely firm, and not willing to back down from your demand for respect. Let him see from your attitude that you're serious, not joking or hysterical.
Your intent is not to attack him -- it is only to set proper boundaries. You want to let him know in no uncertain terms, that the workplace calls for propriety at all times, even in the break-room or lounge. But keep your message as brief and comprehensible as possible.
Opening the door to allow excuses on his part, only suggests that you are not absolutely sure of his guilt. And if he doesn't apologize or show proper conduct in the future, it is time to file a complaint.
The key is, pinpoint the problem, then pinpoint the solution:
Problem : "You're staring at me."
Solution : "Stop it."
Problem : Co-worker is harassing me.
Solution : File a formal complaint.
If the guy really is "usually nice", then you may be able to address the problem with him personally, as illustrated above.
But if the guy is a "creep", it may be necessary to file a formal complaint with your supervisor, in order to set the proper boundaries.
As I see it, in this and many other cases, solving ambiguity is the key issue. The presumed guilty party may be purposefully acting in an ambiguous manner, which may seem abusive or may just be some sort of misunderstanding between the parties involved. But you have no control over their actions, so your role is to decide for yourself what is really happening.
You can take the position that they are indeed guilty, in which case you need to address the presumed abuse in a timely and self-confident manner.
Or, you can give the person in question the benefit of the doubt, at least for the time you need to better acquaint yourself with their true motives.
As I said at the beginning of my answer, and it should bear repeating: it is unwise to presume someone guilty of really serious and embarrassing behavior, without real evidence. Simply feeling annoyed or suspicious about someone, is not enough basis for ruining their reputation.