High-k dielectrics as SrxTi1-xOy (STO) are of great interest for the development of dynamic random access memory devices. The characterization of these nanolayers is important. Secondary ion mass spectrometry (SIMS) depth profiling through TiN and STO films is affected by strong artifacts in different ways. The erosion process causes surface topography modifications both in the TiN/STO/TiN layer system and in the silicon substrate. Atomic force microscopy analyses have been carried out on pristine TiN and STO film surfaces and at various crater depths. Very different roughness evolutions are identified for TiN or STO films, within the SIMS craters sputtered with 500 eV Cs+ while using eucentric stage rotation.