Since the 1960s, thicknesses and compositions of thin-film specimens have been determined by using the nondestructive technique of electron probe microanalysis. This approach, refined in the 1990s, is based upon models of the ionization depth distribution, the so-called ϕ(ρz) distribution, and is capable of analyzing layered specimens. Most of these quantification models have led to commercial programs. However, these programs may have possible limitations: some may not be directly compatible with modern computers, they often are “black boxes” making it difficult to assess the reliability of the results, and they are sometimes expensive enough to restrain many labs from purchasing them. We present a user-friendly, free, open-source program, BadgerFilm, implementing a documented ϕ(ρz) model and algorithms allowing the quantification of stratified samples. The program has the ability to calculate absolute X-ray intensities that can be directly compared with Monte Carlo simulations. We give a detailed explanation for the operation of the employed ϕ(ρz) model in thin films. A wide range of detailed Monte Carlo simulations and experimental data have been used to evaluate and validate the accuracy of the implemented algorithms. BadgerFilm demonstrated excellent quantification results for the films and in many cases for the substrates.