A major challenge regarding the characterization of multilayer films is to perform high-resolution molecular depth profiling of, in particular, organic materials. This experimental work compares the performance of C60 + and Ar1700 + for the depth profiling of model multilayer organic films. In particular, the conditions under which the original interface widths (depth resolution) were preserved were investigated as a function of the sputtering energy. The multilayer samples consisted of three thin δ-layers (~8 nm) of the amino acid tyrosine embedded between four thicker layers (~93 nm) of the amino acid phenylalanine, all evaporated on to a silicon substrate under high vacuum. When C60 + was used for sputtering, the interface quality degraded with depth through an increase of the apparent width and a decay of the signal intensity. Due to the continuous sputtering yield decline with increasing the C60 + dose, the second and third δ-layers were shifted with respect to the first one; this deterioration was more pronounced at 10 keV, when the third δ-layer, and a fortiori the silicon substrate, could not be reached even after prolonged sputtering. When large argon clusters, Ar1700 +, were used for sputtering, a stable molecular signal and constant sputtering yield were achieved throughout the erosion process. The depth resolution parameters calculated for all δ-layers were very similar irrespective of the impact energy. The experimental interface widths of approximately 10 nm were barely larger than the theoretical thickness of 8 nm for the evaporated δ-layers.