It's funny you ask. I just got three estimates done to fix a small bubble on the rear fender-well of my 96 civic. Here's what the guys told me.
The first step that needs to be done is to prep the area in question. They do this usually with sand blasting. If the metal is strong enough so that the sand does not blow holes through or if the rust has not gone through the metal, it can be Bondo'd, painted and sent on its way. Total cost was about $150
If there are small holes or a large hole, the area will need to be cut out with a new section put in its place. This requires cutting, welding, grinding, etc. This raises the price to about $500.
Most places will not guarantee the rust repair either. If it should happen to rust again two years down the road because of galvanic corrosion (two dissimilar metals welded together) you are again out another $500. In talking to the guys, all agreed that if I did it now, or if I waited three years, it would still cost the same.
Keep in mind, the spot on my car is about the size of two dimes placed next to each other.