It is difficult for brittle materials to acquire high machined surface quality as they have low fracture strength. But in the case of nanometric cutting technology, nanometer level machined surface is often acquired by means of ductile material remove mode. In order to investigate physical essence of ductile machining process, this paper carries out molecular dynamics (MD) analysis of nanometric cutting single crystal silicon. The result shows that huge hydrostatic pressure induced in the local area which lead to the silicon atom transform from classical diamond structure (α silicon) to metal structure (β silicon). At the same time, the stress concentration is avoided by uniformly distributed pressure in the cutting area. These two important factors together result in the ductile machining of silicon and then acquire super-smooth surface.