The influence of the substrate topography on the morphology of DPPC and POPE lipid layers was studied by atomic force microscopy. Phase imaging was used to distinguish between the hard supporting substrate and the soft lipid layer. Epitaxially grown SiGe films as well as ion bombarded SiGe and GaSb films served as templates for lipid deposition by spin coating. On templates with structures having high aspect ratios, lipid bilayer formation is difficult, whereas lipid layers conform very well to shallow, structured templates. The surface topography of the underlying substrate is well visible on top of the lipid layers. DPPC lipid terrace edges align to small grooves (dislocation lines) of the SiGe template, when the samples are exposed to high humidity at elevated temperatures. Lateral alignment across a distance of up to 5 micrometer as well as alignment of terrace edges on top of a 75 nm high lipid island has been observed. In the case of very low lipid coverage, the 100 nm x 100 nm pits of a nanofaceted SiGe film as well as the shallow troughs of an ion eroded SiGe film act as preferential deposition sites for lipid bilayers resulting in arrays of POPE nanostructures on the surface. The contact angle of water on structured substrates is reduced from roughly 70° to typically 50° due to DPPC deposition.