To assist the development of plasma processes to pattern graphene in a controlled way, interactions between hydrogen plasma species (H, H+, H2 +) and various types of graphene surfaces (monolayer, nanoribbons, multilayer) are investigated using atomic-scale simulations. It is shown that only “hot” H particles (i.e., with a kinetic energy greater than ~0.4 eV at 300 K) can adsorb on the basal plane of surface-clean graphene while adsorption is barrierless on free edges or vacancies. Surface reaction probabilities (reflection, adsorption, penetration) are found to strongly vary with the incident species energy, which allows to determine specific energy ranges (or process windows) for different types of H2 plasma treatment: lateral etching of graphene nanoribbons (GNRs), cleaning of graphene surfaces or vertical etching of multilayer graphene (MLG) stacks. Molecular dynamics simulations of GNRs trimming in downstream H2 plasmas allow to understand the mechanism which governs the anisotropic etching of ribbons and explains the absence of line-edge roughness on their edges. Interactions between low-energy (5–25 eV) H x + (x = 1, 2) ions with MLG are also investigated. Ion-induced damage (hydrogenation of successive graphene sheets, creation of vacancies) and etching of the MLG stack are found to vary with the ion energy, the ion fluence and the ion composition.