It depends on the rust. If it isn't rusted all the way through, you can usually use a wire wheel to remove the rust, treat it with a rust converter (like Ospho, just to be safe), prime, prime with high-build primer, sand, prime again, sand again . . . then paint.
If it's rusted through, you'll need to cut out the old metal and weld in new metal patches, grind down the welds, fill with bondo, prime, sand, prime, sand again . . . then paint.
Sometimes what appears to be surface rust is really rust coming through from the inside, so using the wire wheel will expose that (when you begin to see light coming through from the other side - you know you have more than surface rust).