We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.