Is it rusted over the paint or rusted under the paint? For the former they make iron decontaminate spray to remove iron particles embedded in the paint. For the latter, you'd want to sand it down to clean metal and then prime and paint.

The paint should act as the sealer as long as you touch it up if it ever gets knocked off again. Little rust spots on what I assume to be the hood or front of your car are really a non-issue, corrosion-wise. But that said, are these just small spots on body panels, or are they spots near wheel wells or something where water tends to collect?

You would have to get a grinder and basically grind them out and refill them and paint over them. It's pretty hard to get rid of it because it's oxidation so it's creating a new chemical compound with the material that the good is made of. I'd probably just get a sander, sand it down to where most of its gone without putting a depression in it, and then paint over it with two or three coats of paint. Then wait a year, sand it back down and paint over it again if it starts to flake, but if you sand it down well you probably won't have to worry about it again. Not a huge deal, having rust on the frame can be bad though.