Molecular dynamics (MD) simulations of monocrystalline copper (100) surface during nanomachining process were performed based on a new 3D simulation model. The material removal mechanism and system temperature distribution were discussed. The simulation results indicate that the system temperature distribution presents a roughly concentric shape, a steep temperature gradient is observed in diamond cutting tool, and the highest temperature is located in chip. Centrosymmetry parameter method was used to monitor defect structures. Dislocations and vacancies are the two principal types of defect structures. Residual defect structures impose a major change on the workpiece physical properties and machined surface quality. The defect structures in workpiece are temperature dependent. As the temperature increases, the dislocations are mainly mediated from the workpiece surface, while the others are dissociated into point defects. The relatively high cutting speed used in nanomachining results in less defect structures, beneficial to obtain highly machined surface quality.