A Good Filler Primer

I know of one fail proof way to fix rust pits for good and not have to worry about the filler cracking, using the obsolute ways of the past--Lead filler. I don't know how much room you have to work, but to use lead you need to sand blast or wire brush to absolute clean rust free metal, than heat and tin the metal to accept the lead filler then heat the lead and paddle it into place. If this is an option, you'd need to buy the tools, files, tinning compound, wood paddles and a lead rated dust mask. Considerations are cost, safety--you don't want a torch near fuel lines or tanks and how much labor you want to put in it. Plus the heat will ruin the surrounding paint and it will need to be removed near the repair and feather edged back to good paint if there is still good surounding paint. I know where you can buy a kit with most materials if this is the way you want to go. I have used it many times on sheet metal where the thiness of the metal requires care that you don't overheat and warp it. An old rusty mustang that i wanted a permant fix for. If i can help let me know.

For metal that i can't practically remove the rust, i use Por 15 rust paint over the rusty metal, than use the same modern materials as Rod mentioned. Epoxy primer is a must as it will waterproof the filler and stop rerusting. Before epoxy, filler was applied to bare metal and water could go thru from the backside of the repair. In example a dent pulled from a fender than filled with plastic filler, Filler would absorb water like a sponge through the holes left by the dent puller and rust would bubble around the repaired area even if the back was painted as regular paint is porous. Now you can use body filler on top of epoxy primer and sandwich it between coats to make it water proof.

Currently i am using Por 15 on a dozer under carriage because the paint is always worn away by sand kicked up by the tracks. So it makes little sense to sand blast all the rust off. The por 15 is very tough and will wear off much slower, extending the time between repaints. You can try brazeing over pits too but it is much harder to sand/file than lead. Also i have heard of JB weld used to fill pits, it too is tough to sand and i don't know if it will stick on top of epoxy primer. Pits are a tough repair, but it can be done to like new.

This is how I would approach any serious pitting (>>0.005"):

1. Sandblast to bright metal.
2. Epoxy prime with a product similar to PPG OMNI MP170.
3. Spread a two-part "flowable polyester filler" such as 3M Flowable Finishing Putty where needed (this stuff is the same as smooth plastic filler (w/o fiberglass strands) but is a little more fluid in consistency).
4. Rough sand with 80 grit.
5. Reprime completely with epoxy.
6. Spray a two-part surfacer such as OMNI MP182 (use 1-part OMNI MP181 or 281 if you cannot safely deal with isocyanates) - about 4 coats.
7. Sand with 220 grit.
8. Repeat 6 as needed to obtain a smooth, defect free surface. You can use an acrylic spot putty sparingly on minor imperfections at this point but if used you should cover with the surfacer (after complete dry) to provide a uniform colored surface for the topcoat.
9. Final sand with 400 grit.
10. Clean and tack off
11. Topcoat

If sandblasting is not a realistic option, then wirebrush well after all old paint removal and use a rust converter such as Extend Rust Treatment as an alternative to step 1. POR15 as noted by Dozerboss in one of his posts below would be another such product but I have no personal experience with it.

The above brand names are the ones I have used successfully. Other manufacturers have similar products equally well suited to the same job.

I know this sounds like a lot of effort but rust pits are frustrating to deal with. There's no quick fix here. It all depends on how smooth you want it to wind up being.

Rod