Before you set to work, remember how sneaky rust can be. What looks like surface rust can, after some grinding, reveal itself to be something a lot worse. If you're prepared for the unexpected, then here's how it's done:
Grind or sand. Start by removing all traces of rust from the area. The easiest and most thorough way to do this is with an electric metal grinder. If you choose this option, remember that sparks and debris can fly, so follow the safety procedures closely, covering all areas of your body, especially your hands and face. Use a 16- to 24-grit sanding disk. Hold the tool firmly and touch the grinding tip to the rust very gently, moving the tool slowly back and forth over the affected area and checking your progress frequently until the rust is removed.
If there's less than a square inch (2.5 square centimeters) of rust on the surface, using heavy-duty sandpaper (80-grit or less; for best results, use a sandpaper block) should work fine. You can use a sandpaper pen for the smaller spots. Whatever you choose, make sure there are no ragged edges--the ground or sanded metal should segue into the surrounding painted surface smoothly. Use a finer sandpaper (120- or 200-grit) to smooth down any rough spots. Finally, clean the area of any sanding dust or debris.
Fill the area. There are several body fillers available, many of which serve multiple purposes like inhibiting rust (a definite must) or acting as a primer coat for your paint. Ask the retailer what he or she recommends, and follow the package directions for application, drying time, and sanding. If you're filling a hole, remember the size limit: Anything larger than an inch (2.5 centimeters) will need a professionally welded or bolted metal backing.
Prime and paint. Once the filler is sanded down, apply primer (if necessary) and paint using the same methods detailed in Step 2.
If your affected area is large and you want to apply paint the quick way--directly from an aerosol spray can--be aware that this method is messy and inexact. To make it less so, tape newspaper so it butts up and borders the area completely, with at least a 2-foot (61-centimeter) radius on all sides. Cover the rest of your car with a protective material, like a sheet or tarp. Follow the directions for application. When you're done, the painted area will dry slightly raised from the surrounding surface, so you'll need to sand or buff it to smooth it out. Finally, polish, step back, and admire your work.
As you continue on in your driving life, remember that an ounce of prevention (wash and wax!) equals a pound of cure. Keep an eye out for scratches and rust spots, make your repairs promptly, and the world will be a slightly less unpredictable place.