With the development of semiconductor industry, the polishing method has already became the main stream technique in realizing the global flatness. Because of lacking investigation physical essence of polishing, the prediction power and robustness of today's material removal model is poor. In order to understanding micro-mechanism underlying planarization, the author carried out computer simulation of nanometer polishing aluminum with vacancy using molecular dynamics (MD) method. In this paper, the author investigated mechanical deformation and the machined surface integrity of crystal materials, after that explains the micro-mechanism of nanometer polishing process