A three-dimensional model of molecular dynamics (MD) was employed to study the nanometric machining process of Si. The model included the utilization of the Morse potential function and the Tersoff potential function to simulate the interatomic force between atoms. By analysis of snapshots and local radial distribution function (RDF) during the various stages of the cutting process, amorphous phase transformation of chip and machined surface are observed, but no phase transformation of bulk. Chip volume change is observed due to the amorphous phase transformation. Dislocations around the tool and elastic recovery of the machined surface do not appear. The effects of surface adsorption on machined surface state have been studied on the basis of surface energy and surfaces hardness. Surface energy decreases and hardness increases by adsorption. Oxygen atoms adsorbed are on the machined surface and subsurface region.