A three-dimensional model of molecular dynamics (MD) simulation was employed to study the generation process of nanometric machined surfaces of monocrystalline copper. The model included the utilization of the Morse potential function to simulate the interatomic force between Cu-C and Cu-Cu. By analyses of the MD simulation snapshots of the various stages of the nanometric cutting process and local radial distribution function (RDF), the structure of the bulk and the machined surface with no change and that of the chip with minimal change were observed. Potential energy had significant fluctuations due to generation and propagation of dislocations around the tool. The elastic recovery along the machined surface of the work material was observed after the tool passed. Because the state of machined surface was an important influence on the performance and the physical and chemical properties of product, the effects of surface relaxation on the machined surface state were investigated under the vacuum condition.