The microstructure and surface topography of PVD hard coatings are among the most important properties, as they significantly determine their mechanical, tribological and other properties. In this study, we systematically analyzed the microstructure and topography of a TiAlN/CrN nanolayer coating (NL-TiAlN/CrN), not only because such coatings possess better mechanical and tribological properties than TiAlN and CrN monolayer coatings, mainly because the contours of the individual layers, in the cross-sectional STEM or SEM images of such coatings, make it easier to follow topographic and microstructural changes that occurred during its growth. We investigated the effects of the substrate rotation modes on the microstructure and surface topography of the NL-TiAlN/CrN coating, as well as on the periodicity of the nanolayer structure. The influence of the substrate material and the ion etching methods were also studied, while special attention was given to the interlayer roughness and influence of non-metallic inclusions in the steel substrates on the growth of the coating. The topographical features of the NL-TiAlN/CrN coating surface are correlated with the observations from the cross-sectional TEM and FIB analysis. Selected non-metallic inclusions, covered by the NL-TiAlN/CrN coating, were prepared for SEM and STEM analyses by the focused ion beam. The same inclusions were analyzed prior to and after deposition. We found that substrate rotation modes substantially influence the microstructure, surface topography and periodicity of the NL-TiAlN/CrN layer. Non-metallic inclusions in the substrates cause the formation of shallow craters or protrusions, depending on their net removal rates during the substrate pretreatment (polishing and ion etching), as compared to the matrix.