The Plan

• Before repairing any kind of rust damage, you need to bear in mind that rust is like cancer; it can start as one small spot and will spread everywhere given enough time. As such, getting rid of every last bit of oxidation is crucial, and simply removing that which is visible on the surface will only invite disaster in the future.
  Rust almost always starts from the back of a panel and moves outward, so removing and replacing the affected area is the only way to stop its spread.
  
  

Identifying the Rust.

• Wherever you see rust, start by stripping away the paint with a media-blasting agent (like sand or ground-up walnut shells) or chemical paint stripper like those made by 3M. Once all of the visible rust is exposed, tap the area around it with a small-headed hammer to identify weak spots. If the metal dents in a smooth conical shape, it's good, and any cracking or puncture will indicate rust. Don't be afraid to give the metal a sharp rap; you've got plenty of bodywork ahead of you anyway, so a little dent in the good metal isn't going to be your biggest problem.
  
  

Removal

• Wherever you identify rust, mark the area with a permanent marker. Measure out a rectangle on the metal surface that covers the rust, and remove it with a cut-off wheel. Cut no more than 1/4 inch into the panel, or you risk damaging underlying components.
  
  

Installing the Patch

• You can cut your patch panel from either a new/replacement panel, or fabricate one yourself if you have the skill to do so. Cut your patch panel to 1/2-inch larger than the hole, and then cut it in half. Twist one of your new half-panels so it fits into the hole and position it on one side. Tack weld into place, and do the same thing with the other side. You can use a strong magnet to position the second panel and hold it in place. This method is but one of several used for different areas and applications, so by all means butt-weld or overlap the panel as you must.
  
  

Finishing

• Tack weld your replacement panels into place with small welds placed at 3/4-inch intervals, and grind the welds down when you're finished. You'll now have a solid substrate for polyester body filler and future bodywork, but that's a whole 'nother article.