Molecular dynamics (MD) simulation can play a significant role in addressing a number of machining problems at the atomic scale. This simulation, unlike other simulation techniques, can provide new data and insights on nanometric machining; which cannot be obtained readily in any other theory or experiment. In this paper, some fundamental problems of mechanism are investigated in the nanometric cutting with the aid of molecular dynamics simulation, and the single-crystal silicon is chosen as the material. The study showed that the purely elastic deformation took place in a very narrow range in the initial stage of process of nanometric cutting. Shortly after that, dislocation appeared. And then, amorphous silicon came into being under high hydrostatic pressure. Significant change of volume of silicon specimen is observed, and it is considered that the change occur attribute to phase transition from a diamond silicon to a body-centered tetragonal silicon. The study also indicated that the temperature distributing of silicon in nanometric machining exhibited similarity to conventional machining.