Tiny details of the phospholipid (DMPC) membrane morphology in close vicinity to nanostructured silica surfaces have been discovered in the atomic force microscopy experiments. The structural features of the silica surface were varied in the experiments by the deposition of silica nanoparticles of different diameter on plane and smooth silica substrates. It was found that, due to the barrier function of the lipid membrane, only particles larger than 22 nm in diameter with a smooth surface were completely enveloped by the lipid membrane. However, nanoparticles with bumpy surfaces (curvature diameter of bumps as that of particles <22 nm) were only partially enveloped by the lipid bilayer. For the range of nanostructure dimensions between 1.2 and 22 nm, the lipid membrane underwent structural rearrangements by forming pores (holes). The nanoparticles were accommodated into the pores but not enveloped by the lipid bilayer. The study also found that the lipid membrane conformed to the substrate with surface structures of dimensions less than 1.2 nm without losing the membrane integrity. The experimental results are in accord with the analytical free energy model, which describes the membrane coverage, and numerical simulations which evaluate adhesion of the membrane and dynamics as a function of surface topology. The results obtained in this study are useful for the selection of dimensions and shapes for drug-delivery cargo and for the substrate for supported lipid bilayers. They also help in qualitative understanding the role of length scales involved in the mechanisms of endocytosis and cytotoxicity of nanoparticles. These findings provide a new approach for patterning supported lipid membranes with well-defined features in the 1.2-22 nm range.