Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a high performance tool for molecular depth profiling of polymer films, in particular when they are structured in microphases. However, a major issue is the degradation of polymer materials under ion irradiation in reactions such as cross-linking, chain breaking, or reorganization processes of polymers which have been demonstrated for materials such as polystyrene (PS) and poly(methyl methacrylate) (PMMA). This work aims at comparing ToF-SIMS molecular depth profiling of structured polymers (polystyrene (PS)-b-polymethyl methacrylate (PMMA) block copolymers (BCP)) using either ultralow energy cesium or the more recently introduced C60(++) (under NO dosing and with sample cooling) and argon cluster ion beams (using Ar-1500(+) ions at 5 keV). The latter improved the quality of the depth profiles, especially the argon cluster ion beam, as it is characterized by a greater homogeneity for the sputter yields of PS and PMMA. No significant artifacts were observed, and this was confirmed by the comparison of depth profiles obtained from films with variable thickness, annealing time, and morphology (cylindrical blocks vs spherical blocks). Comparison to a theoretical model (hexagonal centered pattern) ensured that the ToF-SIMS depth profiles described the real morphology and may thus be a relevant characterization tool to verify the morphology of the films as a function of the deposition parameters