Molecular dynamics simulations are performed to verify the effect of grain boundary on nanolithography process. The model with about two hundred thousand copper (Cu) atoms is composed of two different crystal orientations of which contact surfaces are (101) and (001) planes. The grain boundary is located on the center of model and has 45 degreeangle in xz-plane. The tool is made of diamond-like-carbon with the shape of Berkovich indenter. As the tool is indented and plowed on the surface, dislocations are generated. Moreover, during the plowing process, the steps as well as the typical pile-ups are formed in front of the tool. These defects propagate into the surface of the substrate. As the tool approaches to the grain boundary, the defects are seen to be accumulated near the grain boundary. The shape of the grain boundary is also significantly deformed after the tool passes it. We observed the forces exerted on the tool by the contact with substrate, so that the friction coefficients can be obtained to address the effect of the grain boundary on the friction characteristics.