Precise positional control of surface chemical reactions can be used to fabricate nanometer scale surface features. Scanning probe techniques have demonstated the ability to manipulate the structure of surfaces atom-by-atom. We use quantum chemical methods to model several chemically active scanning probe processes for modifying diamond and Si surfaces using chemically active species attached to scanning probes. We include a comparison of the effects of cluster size on reaction barriers and enthalpies. We also compare the effects of method on reaction barriers, enthalpies and structure. Our results indicate that given the technology to synthesize the chemically active species on scanning probe, surface structure can be modified at the atomic scale using only mechanochemical mechanisms.