Surface morphology has been demonstrated to influence the tribological properties at different scales, but the phenomena which occur at the nanoscale have not been completely understood. The present study reports on the effect of focused ion beam nanopatterning on coefficient of friction (CoF) and adhesion of Si(001) surface covered by native oxide. Regular, arrays of nanogrooves reduce both CoF and adhesion, related to a hydrophobic character of the patterned surface, but this effect disappears as soon as the separation among the nanostructures approaches the microscopic scale. The dependence of this hydrophobic effect on the pitch is not linked to the corresponding contact area. It has been found that each nanostructure is surrounded by a low-friction region which extends some hundreds of nanometers from it. For pitches of 125 and 250 nm these low friction regions completely overlap, generating a consistent decrease in CoF and adhesion, while for pitches of 500 and 1000 nm their effect is negligible. The low-friction regions were not observed in humidity-free ambient, indicating that they are the origin of patterns of hydrophobicity.