This study reports the atomic structure and nanoscale morphology of monolayer graphene sheets and nanotubes on an insulating SiO₂ substrate with a conducting back gate. Using scanning probe microscopy, the researchers reveal that the graphene sheet's hexagonal lattice symmetry is disrupted by spatially dependent perturbations, which are partially aligned with the underlying SiO₂ substrate. These effects are obscured by photoresist residue from standard lithographic methods, which must be removed to expose the intrinsic structure of the graphene. The study shows that the graphene sheet is clean at the atomic scale after a novel cleaning process, enabling detailed structural analysis. Atomic-resolution images reveal both triangular and hexagonal lattice patterns, indicating significant electron wave scattering. The thickness of the graphene film is found to be 4.2 Å in ultra-high vacuum (UHV), compared to 9 Å in ambient conditions, suggesting the presence of atmospheric species. The 3D morphology of the graphene sheet is analyzed, showing that it is approximately 60% smoother than the SiO₂ surface. The height-height correlation function indicates that the graphene surface has short-range correlations, consistent with its underlying SiO₂ substrate. The observed corrugations are attributed to the graphene conforming to the SiO₂ substrate rather than intrinsic structural instability. The study also shows that resist residues are common on lithographically-fabricated graphene devices and must be considered in interpreting transport and structural measurements. The findings suggest that the corrugations in graphene on SiO₂ are due to partial conformation to the substrate, not intrinsic corrugation. The results highlight the importance of understanding the atomic and nanoscale structures of graphene in its measured configuration to explain transport properties. The study demonstrates a novel combined SEM/AFM/STM technique for resolving atomic structures of oxide-supported graphene-based electronic devices. The technique enables the characterization of clean graphene sheets and provides insights into the impact of atomic-scale defects and adsorbates on nanoscale transport properties. The findings have implications for future studies on graphene's behavior on different substrates and the development of new experimental approaches to investigate the effects of corrugation-induced strain on graphene's transport properties.This study reports the atomic structure and nanoscale morphology of monolayer graphene sheets and nanotubes on an insulating SiO₂ substrate with a conducting back gate. Using scanning probe microscopy, the researchers reveal that the graphene sheet's hexagonal lattice symmetry is disrupted by spatially dependent perturbations, which are partially aligned with the underlying SiO₂ substrate. These effects are obscured by photoresist residue from standard lithographic methods, which must be removed to expose the intrinsic structure of the graphene. The study shows that the graphene sheet is clean at the atomic scale after a novel cleaning process, enabling detailed structural analysis. Atomic-resolution images reveal both triangular and hexagonal lattice patterns, indicating significant electron wave scattering. The thickness of the graphene film is found to be 4.2 Å in ultra-high vacuum (UHV), compared to 9 Å in ambient conditions, suggesting the presence of atmospheric species. The 3D morphology of the graphene sheet is analyzed, showing that it is approximately 60% smoother than the SiO₂ surface. The height-height correlation function indicates that the graphene surface has short-range correlations, consistent with its underlying SiO₂ substrate. The observed corrugations are attributed to the graphene conforming to the SiO₂ substrate rather than intrinsic structural instability. The study also shows that resist residues are common on lithographically-fabricated graphene devices and must be considered in interpreting transport and structural measurements. The findings suggest that the corrugations in graphene on SiO₂ are due to partial conformation to the substrate, not intrinsic corrugation. The results highlight the importance of understanding the atomic and nanoscale structures of graphene in its measured configuration to explain transport properties. The study demonstrates a novel combined SEM/AFM/STM technique for resolving atomic structures of oxide-supported graphene-based electronic devices. The technique enables the characterization of clean graphene sheets and provides insights into the impact of atomic-scale defects and adsorbates on nanoscale transport properties. The findings have implications for future studies on graphene's behavior on different substrates and the development of new experimental approaches to investigate the effects of corrugation-induced strain on graphene's transport properties.