The atomic structure of epitaxial single and bilayer graphene on Ru(0001) was studied by scanning tunneling microscopy (STM). High-resolution imaging of the surface of single layer graphene shows a moiré with pronounced buckling and broken A/B carbon sublayer symmetry due to a strong interaction with the metal substrate. The top sheet of bilayer graphene is largely unperturbed by residual interactions with the substrate. Screened from the metal substrate, it shows the hallmarks of freestanding monolayer graphene: a honeycomb structure with equivalent carbon sublattices imaged in STM and a linear dispersion of bands near the Dirac point