The sliding friction between a rigid tip and an amorphous polymer film is studied using large scale molecular dynamics simulation. We focus on the changes of surface microstructure on the polymer film caused by friction, and study the effects of the interaction between tip and substrate, the sliding speed and the molecular chain length on the change of surface microstructure. When there is an adhesive force between tip and substrate, the bond reorientation caused by friction occurs in the sliding region of polymer substrate, and radius of gyration of the molecular chains on the surface layer of polymer substrate elongates along the sliding direction. Moreover, the extent of surface microstructure changes increases with the decrease of sliding speed. During the process of microstructure changes caused by friction, the chain loops and chain ends make different contributions, leading to different deformation mechanisms of molecular chain. The drag action between the tip and chain end monomers plays a more important role in making molecular chains deformation, when the degree of entanglement of polymer substrate becomes greater or when the sliding speed of tip becomes lower. Our results also show that change of surface microstructure is a key mode of friction energy dissipation in this tip and polymer film tribology system.