Filling sheet metal and filling fiberglass are two completely different things.
If you just have some small screw holes that don't go all the way through the top, then the fix is easier. I think the approach depends on whether you are keeping and matching the factory texture or if you will be going with a smooth top. With a smooth top, the strategy zimmer describes is great, although possibly overkill if they are just small holes (he may be thinking of fixing Corvettes and not the massive slab of fiberglass that is the back of your hardtop or he may know better than me). If you want the texture, I would keep the repair area smaller, just fill them up with resin, do a minimal sand when it cures, prime and then paint.
You can use polyester fillers if you are just filling small holes and it's not a structural thing. Dura Glass or Bondo-glass are just polyester (Bondo) with glass fibers in them and they will work, but are just harder to get smooth. I did some work with that on my hard top a few years ago and it is still fine. Basically I filled in the seams between the top and lower portions of the shell to make it smooth all over. There's a thread in the body shop if you're interested, but my point is just that is hasn't cracked or fallen off yet or anything.