Unlike conventional two-dimensional (2D) semiconductor superlattices, moiré patterns in 2D materials are flexible and their electronic, magnetic, optical, and mechanical properties depend on their topography. Within a continuous+atomistic theory treating 2D materials as crystalline elastic membranes, we abandon the flat-membrane scenario usually assumed for these materials and address out-of-plane deformations. We confront our predictions to experimental analyses on model systems, epitaxial graphene, and MoS2 on metals and reveal that compression/expansion and bending energies stored in the membrane can compete with adhesion energy, leading to a subtle moiré wavelength selection and the formation of wrinkles.