We use STRATAGem* for processing our multi voltage analysis (MVA) EPMA data to obtain both composition and thickness on thin films deposited on various substrates. However, if an element is present in both the film and substrate the film thickness or composition must be specified. Multiple layers can also be accommodated.
Here is the Probe for EPMA k-ratio export window for STRATAGem* reprocessing:

Here are the results for a thin film calculation in STRATAGem*:

The document attached below will be of assistance in exporting STRATAGem* results to Excel.
More discussion on thin film analysis in PFE can be found here:
http://probesoftware.com/smf/index.php?topic=111.0* © Copyright 1993-2016 SAMx