For rust, the most important thing to remember is to eradicate all the corrosion on your first try. If you don't, you'll be chasing that same rust spot for the life of the vehicle or the rest of your life, whichever comes first. Here are the basic steps to follow:

1. Using tin snips or a drill and a course file, remove about 1/8" to 1/4" of the metal around the hole so that there is solid metal surrounding it. If you just have a few pin holes, you don't need to cut-out the metal.
2. Completely removing the rust from the metal surface is the most important step of body repair, unless you are using special paint that is designed to paint over rust (such as POR-15, which I recommend). Avoid "rust conversion" primers; they generally don't work. Otherwise, take a piece of 60 or 80 grit sandpaper or a wire brush (wire brush then sandpaper works the best) and clean up the metal areas that were exposed in step 1 (on both sides, if necessary). Sand until you see shiny metal and then scrap again with your scraper to ensure the metal is solid metal and not metal over the rust. Keep sanding and scraping until you are down to solid, shiny metal
3. Gently sand using a finer sandpaper (150 - 220 grit) and feather out into the good paint surrounding the affected area until you can see the spread of the layers of paint (bare metal-primer-color coat-clear coat).
4. With a plastic brush, scrub and clean the area with soap and water and dry thoroughly. Dish washing detergent (such as Dawn) works well.
5. If you are not using a special paint-over rust paint, you must use a rust remover compound to remove the rust from the pitted areas that can't be reached by sandpaper. There are easy to use gels such as "Naval Jelly" or powders that have to be mixed with water such as "Rust Raise". "Naval Jelly" or equivalent can be found at most auto parts stores and is easier to apply because it stays where you put it. Follow the instructions on the package and apply more than once until all of the visible rust is gone, but don't allow it to get onto the painted surfaces that you don't intend to repaint. Mask the area from the rest of the panel using masking tape and paper if you want to. "Naval Jelly" leaves a white powder on the metal after washing it off. Scrub this off with a plastic brush or sandpaper to see the metal below. Use clean 100 - 150 grit sandpaper between applications to make sure no rust is hiding beneath the surface. It is vital that all the rust be removed otherwise it will "crawl" underneath the new paint and you will be back to square one.
6. When all rust has been removed, sand the surface one last time with a clean piece of 150 - 220 grit sandpaper and scrub and clean the area with soap and water and dry thoroughly. Use a heat gun or hair dryer to ensure the surface is completely dry, and allow the surface to cool for a few minutes. Don't wait too long before applying the first coat of primer because the bare metal begins reacting with the oxygen in the air immediately which starts the formation of rust.
7. Patch holes with a fiberglass patch kit.
8. Fill with polyester filler (such as "Bondo")

Links:
Removing rusted bolts
Rust Never Stops