1. Considering the average atomic number of your described thinfilm is relatively high, depending how thick the thinfilm is you might be able to directly measure the compositions of the film with WDS/EDS without going through corrections by using low acceleration voltage. Run some Monte Carlo simulations (CASINO) to estimate the interaction volumes using different voltages.
2. If the interaction volume is bigger than the thickness of the film even at the lowest possible acceleration voltage, then you will need help from software designed for thinfilm analysis like StrateGem. There are tutorials online explaining the principles of thinfilm analysis and I wont go into that.
Recently, there is such called Soft-Xray Emission Spectroscopy (SXES) attached to the EPMA column. This can measure composition or mapping for the thin film. I have tried it with 50nm Au thin film without any problem.