Metal rust is the biggest enemy to anyone who has made an investment into their car. Metal rust will quickly turn a valuable car into a candidate for the scrap heap. If you discover rust on your car during a project, you need to use a wire brush or wheel attachment to remove all of the surface rust that you can. Once the surface rust is removed, you need to apply a product such as Rust-Mort, from SEM Products. This will convert the rust into a sandable and paintable polymer and stop future rusting in that portion of the metal.
For more info, see Self Etching Primer vs Epoxy Primers