I agree with malc, but you can remove rust with grinder disks, wire wheels, etc. and then use a "rust convertor" or "metal conditioner" as added protection. It's your choice how you get back to "shiny" metal, and how you repair any holes that are going to appear. I would not recommend using "bondo" to repair any hole. Body putty should only be used as a skim coat to cover small imperfections in solid metal.
Seriously, body putty is like a sponge. If bare putty is exposed to moisture, the paint will bubble quickly. If you want a chance of the rust not returning, there are a few solutions.
1) Sandblast/grind to shiny metal removing all rust from top & underside of channel. Repair any holes. (Weld, paintable seam sealer, anything waterproof) Use a metal conditioner (usually phosphoric acid solution) to keep any rust you didn't grind or sandblast from spreading. Spray with epoxy primer. (wears like iron) Spray paint.
2) Instead of metal conditioner you can spray self-etching primer, and then paint. The self etching primer has rust inhibitors in it, but it is not as durable as an epoxy primer. Most epoxy primers can't be sprayed over etching primers, so you have to pick one way or the other.
Either way will work, but the prep work is the most important.
70 Chevelle 13.7 @ 99.7
70 280 SL Silver/Black top
05 C230 Kompressor
03 Dodge Durango SLT