can you post some pictures
did you clean off all the paint already and now are you looking at small holes, or is the paint still on, if the paint is still on then maybe the holes are bigger and there's more of them than you think, also if you haven't cleaned the area up yet then maybe there's more surprises lurking beneath it, maybe someone's already tried to repair the damage and there's bondo, etc.
here's a tip, park the car in the garage with the lights off and shine a shop light under the car and look in the trunk to see where the light shines through, that way you will be able to detect the smallest pin hole
as far as I know there's only one way to repair rust holes, and that is to cut them out and patch them with new metal
can you post some pictures?