How can I remove rust from my car?

A grinder and/or sand paper.

To fill in any holes left behind by the removal of the rust, use a body filler. Once it is dried, you can sand it so that the surface is smooth and clean. Once it is sanded, you can prime it and pain it to match the colour of your car.

Sand off the loose rust and then make sure you seal it up so it does not rust any further. I use the products by KBS Coatings. They have a system sampler that should work great for you.
http://www.kbs-coatings.com/KBS-RustSeal-C37.aspx

If you live outside of New England, you remove all of the SERIOUSLY rusted metal with cutters and pliers. For minor rust or dealing with the edges of a major area that you cave already got the crap out of, grinding and/or sanding to bare meal is what is called for. Then you seal the edges to ensure that the rust doesn't spread and do the body filler thing.

If you live in New England, you start looking for another vehicle. Once it's started in one place, it spreads like wildfire. You can try to do the above, but my experience is that the odds of it working in any lasting manner are minimal.

This is the oldest question ive ever seen! Seriously 2003? WOW!! Anyways, a wire wheel will work wonders for removing surface rust and it will even get rid of it from the pits caused by extensive corrosion. Sanding to bare metal is rarely the way to completely do it because of said pits. Media blasting will cost you but is superior to all, but a drill mounted wire wheel and lots of patience has always done me well. Rust converters are fucking worthless! And by no means should holes be filled with body filler!!! I did it once when I was 15 and I didnt know any better, and it just wont do! Dont forget about the other side of the rust too!!! Cut out the cancer known as rust and weld in a new piece, which is easier said than done. Ill walk anyone through it and give any more help that I can.