Abstract: Using atomistic simulations we investigate the morphological properties of graphene deposited on top of a nanostructured substrate. Sinusoidally corrugated surfaces, steps, elongated trenches, one-dimensional and cubic barriers, spherical bubbles, Gaussian bumps, and Gaussian depressions are considered as support structures for graphene. The graphene-substrate interaction is governed by van der Waals forces and the profile of the graphene layer is determined by minimizing the energy using molecular dynamics simulations. Based on the obtained optimum configurations, we found that (i) for graphene placed over sinusoidally corrugated substrates with corrugation wavelengths longer than 2 nm, the graphene sheet follows the substrate pattern while for supported graphene it is always suspended across the peaks of the substrate, (ii) the conformation of graphene to the substrate topography is enhanced when increasing the energy parameter in the van der Waals model, (iii) the adhesion of graphene into the trenches depends on the width of the trench and on the graphene's orientation, i. e., in contrast to a small-width (3 nm) nanoribbon with armchair edges, the one with zigzag edges follows the substrate profile, (iv) atomic-scale graphene follows a Gaussian bump substrate but not the substrate with a Gaussian depression, and (v) the adhesion energy due to van der Waals interaction varies in the range [0.1-0.4] J/m(2).