We notice more little things about your character and what you say. We also notice more of the little things that display your intelligence (or lack thereof).
For example a friend of mine had a girlfriend and this is some small thing she did (or didn't do), and it is evidence that she is a thoughtless bitch. It was raining and they had to get into his car and the car was locked. He unlocked her door first so she would not get rained on. When she got in the car and he had to walk around to open his door, she did not have the courtesy to open his door for him. That means he had to take a few more seconds to unlock his door himself and get rained on. WHAT A BITCH!
If we can notice that action (or inaction) explained above, we can definitely notice anything you actually speak of (such as something about your body). Freaking out about your body is not near as bad as the above example because freaking out about your body does not make a girl a bitch, so it's ok. We will notice your self-consciousness and it depends on the guy if he does something about it or if he cares. A nice guy would try to compliment you to make you stop thinking so negatively.
But not every guy actually cares about those little things you do; so he might ignore you intentionally. That could be good or bad depending on how you feel about that. It might not be so bad for a guy to ignore his girl from time to time, because he at least gives you some alone time and doesn't bother you. The guy might also ignore those things you do for his own good. That means he just doesn't want your headaches to become his headaches. So the fact that a guy doesn't say anything or do anything is inconclusive. He could notice and intentionally not say or do anything, or he could intentionally not notice because he doesn't want to know.
Obviously, people know themselves the best, even the little things and everything on our bodies, like scars, stretch marks, etc. Even after they heal, we still know about them, whereas nobody else could ever tell.
I have to agree with the others, most people aren't going to be looking that closely. You get naked and a guy is NOT going to be looking for stretch marks unless he is a freak anyway, lol. Chances are that EVENTUALLY he will notice them but that's usually after you have been together for a fairly extended period of time, have been intimate a while, etc. By then he knows you and undoubtedly has strong feelings for you so while they NOTICE these little "imperfections" they are not hung up on them the way they might be over a hideous wart on your nose, lol. They are just little details of who you are.
You know all the little imperfections that you've got, and unless you pronounce them to others, chances are no one else is going to notice. People aren't looking for flaws on you (unless they're jealous) - they're looking at you because they like what they see.
I get self-conscious as well, but I try to remember that no one else is really paying that close attention to the little things we freak out about.