The molecular dynamics (MD) analysis at the nanometer scale is a powerful tool for understanding the material removal mechanism. In simulating the nanocutting process, various boundary conditions of the workpiece modeling can be applied. The influence of these workpiece boundary conditions (WBCs) to cutting results is systematically studied, including the boundary conditions of only bottom, bottom and cut-in side, bottom and cut-out side, and bottom and both side and full scale WBC or not. The results of the simulation confirm that the boundary condition of bottom and closed cut-out side is best suited to the nanometric cutting process. According to the above-mentioned results of boundary conditions, the MD simulation experiment was carried out with the undeformed chip thickness from 1 to 5 nm. It is indicated that the undeformed chip thickness has strong influence on the cutting, that is, with the deepening of cutting, cutting force becomes stronger, whereas the ratio of the normal force to tangential force becomes less. However the variation of the ratio does not vary much.