Abstract: A three-dimensional molecular dynamics simulation was performed to study the nanometric processing of monocrystal silicon by atomic force microscopy. The two-body Morse potential was used to calculate the force between the workpiece and pin tool,and the tersoff potential was used for simulating the interactions in the monocrystal silicon. The dependence of potential energy and Newtonian layer temperature on the cutting depth was discussed. Meanwhile, the relations of cutting force, clip formation and side flow to the cutting depth were also investigated. At last, a cutting mechanism was proposed.