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With recent developments in carbon-based electronics, it is imperative to understand the interplay between the morphology and electronic structure in graphene and graphite. We demonstrate controlled and repeatable vertical displacement of the top graphene layer from the substrate mediated by the scanning tunneling microscopy (STM) tip-sample interaction, manifested at the atomic level as well as over superlattices spanning several tens of nanometers. Besides the full-displacement, we observed the first half-displacement of the surface graphene layer, confirming that a reduced coupling rather than a change in lateral layer stacking is responsible for the triangular/honeycomb atomic lattice transition phenomenon, clearing the controversy surrounding it. Furthermore, an atomic scale mechanical stress at a grain boundary in graphite, resulting in the localization of states near the Fermi energy, is revealed through voltage-dependent imaging. A method of producing graphene nanoribbons based on the manipulation capabilities of the STM is also implemented.