First off, you don't need to remove all the old paint unless it's failing to stick. Tightly adhered coatings make for great substrate. Same goes for body filler and primer. If it's a good sound coating, no need to take it off. Taking it all off exposes it to flash rust and you likely don't want (or like) that. Epoxy primer is the ONLY thing to put on bare steel.
Now if it's rusting off, then you need to get to bare clean steel. This can be done several ways including blasting, grinding and chemical strippers.
- Blasting is by far the most effective but is also the most expensive
- Grinding with too coarse of an abrasive will cause deep grinding grooves. Too high speed can cause the metal to warp.
- Chemical strippers are effective but very noxious and some require water to rinse which immediately causes rust
Rust that exists in the pitted metal is not a problem as long as you put an epoxy primer on it.
Post some pictures... we like pictures!
Here's a picture of my driver side door after media blasting... the filler will not be removed... no need to remove it to only have to put it back on.