Rust is always worse than it looks. When you start the repair and are grinding and sanding away the rust you will always have to go a little farther than expected. In other words say you have a 3inch hole at the bottom corner of a door, it's all flakey and scalely. When you go in to remove the affected area you'll have to grind and sand a 5 or 6inch area maybe more depending on how far it's spread. You'll need to grind and sand around the area untill you get into clean metal. Be sure to inspect any surrounding bracing and mating pannels. A 4 1/2" grinder with a cupped wire brush works well also the various sanding and griding disks that go with it. Rustolium makes some excelent products for the do it yourselfer. Such as their bare metal primers that have rust proofing qualitys. Personally I'm no fan of the rust removing products such as naval jelly and other chemicals. That's just me though.
Could you post pics of the area? Are you planning on welding in a patch?