Are you meaning that the rust has gone through the panel, or just surface rust?
If the rust has made a hole, then you really should cut the bad sections out and replace them with metal. (Or in some cases, its just easier to replace the whole panel, since you can buy most panels new). Filler should really only be used to fill small imperfections and dents, and even then, using only the minimum amount. if you use it too thickly no only are you not replacing the structure of the car, leaving it weak, but it'll crack and look like crud aswell.
Even if you cant weld, you should be able to cut the panels out, prep it for new bits and get a welder in to weld it up. then finish it off using a small amount of filler.
.. do it once, do it properly. if you dont you'll regret it in the long run
My 2 cents worth
