Can i use an epoxy resin over a polyester filler?

amen to all epoxy!

Yes you can. Epoxy will stick to bondo very well, especially if you rough-up the bondo with 60 grit sandpaper first. It will form a very strong mechanical bond. Epoxy filler will give an even better bond, especially if you and the top layers while the filler layers are still curing. This would provide a superior chemical bond where the layers of epoxy will marry. You can make your own filler with epoxy that you mix first, then add filler material to it. Popular materials to add are microballons, chopped glass strands and colloidal silica. Some people have used homemade alternatives to thicken and extend their epoxy. I've heard of baby powder and corn starch to name a couple. Here's a url for some fillers: http://www.westsystem.com/ss/fillers/

Don't *DON'T* do NOT use bondo on a boat hull. Unless of course you aren't very attached to the boat. It just doesn't hold up in a marine environment. Not to mention which, too often have I seen epoxy repair over poly resin delaminate -- I believe those who say it can be done...I guess it's all about surface prep, but I wouldn't take the chance. Go with the epoxy + microballoons -- especially in areas where appearance is important.

Just stick to a proven system, such as West System, and use what they sell the way they say to do it. Buy the book - it is industry standard! Don't use car stuff on boats - it rarely holds up and is a total pain to fix if it goes wrong.

Epoxy with fiber works well. Several layers depending on how deep the spot start with a high density and finish with a low density for the final faring finish.