a top hat beam is characterized by a uniform intensity distribution, so the fluence is the overall energy divided by the area.

you may want to have a look at https://en.wikipedia.org/wiki/Radiant_exposure

The term flat top is only a qualitative description, without a general formula - to get a better description of the profile you have to take into account also the way it is generated. Better to ask the supplier of the optics. 

For more realistic laser beam, a supergaussian distribution is probably what you are looking for : I=exp(−2(r/w)n). This distribution converges to a top hat for n>>1. The fluence expression will depend on the order n that you choose.