This study reports on the application of secondary ion mass spectrometry (SIMS) for examining thin (20-50 nm) chemically amplified resist films on silicon. SIMS depth profiling was carried out using a gas cluster ion beam to ensure minimal sputter-induced damage to the organic constituents of interest. Specific attention concerned the distribution of the photo acid generator (PAG) molecule within these films, along with the photo-induced fragmentation occurring on extreme ultra-violet photo exposure. Positive secondary ion spectra were collected using a traditional time of flight (ToF)-SIMS and the latest generation IONTOF Hybrid SIMS instrumentation equipped with an OrbitrapTM mass analyzer. Tandem mass spectrometry (MS/MS) capability within the OrbitrapTM secondary ion column was utilized to verify that the C19H17S+ secondary ion did indeed have the molecular structure consistent with the PAG structure. The superior mass resolving power of the OrbitrapTM mass analyzer (∼20× of the ToF mass analyzer) along with improved mass accuracy (a few ppm) proved pivotal in the mass spectral and depth profile analysis of these films. This was not the case for the ToF-SIMS experiments, as the mass spectra, as well as the associated depth profiles, exhibited severe molecular (isobaric) interferences.