Hi Mike,
For thin film work PFE is normally utilized to acquire multiple voltage acquisition (MVA) where the same points are measured using two or more electron beam energies. Because about 80% of my EPMA work is on thin films for material scientists, I have implemented a very easy way to automate the acquisition of this data.
Specifically you simply create a sample setup (and note that oxygen and other non-metals can become a significant issue depending on how the films were deposited and also the native oxide growth time scales), containing the elements of interest.
For example, a student might need to characterize a Bi-Te film on a silicon substrate. So I would normally tune for Bi, Te, Si and O. Then using the New Sample button create, say, three identical samples except that the beam energy is specified at 10, 15 and 20 keV. The exact beam energies may need to be different for particularly thin (< 50 nm) or particularly thick (> 400 nm) films, but 10, 15 and 20 keV beam energies are usually good for films in the range of 50 to 200 nm.
Then one goes to the Analyze! window and select all three samples and click the Add To Setup button. This specifies the three samples as "Sample Setups" which can be assigned to the standards (and unknowns of course). The sample setup assignment is performed in the Automate! window using the Multiple Setups button. Once this is done you will note that the New Sample Basis option is now Use Multiple Digitized Sample Setups.
Then simply start the standard and unknown automation and you will see that the program will acquire each digitized set of points at the three specified beam energies.