Fiber arrays are used to connect arrayed waveguide chips. The end-faces of fiber array components are multi-materials non-uniform surfaces. Their low polishing quality has become a bottleneck that restricts coupling performance of integrated photo-electronic devices. The chemical mechanical polishing (CMP) is normally used to improve the polishing quality of the end-faces of fiber array components. It is very important to optimize process parameters by researching the mechanical behavior of nanoparticles and material microstructure evolution on the CMP interfaces. Based on the elastic and hyper-elastic contact of the soft polishing particle with quartz glass and polishing pad, the material removal mechanism at molecular scale of polishing process for quartz glass using soft polishing particles is investigated, and the material removal rate model is also derived by using Arrhenius theory and molecule vibration theory. Theoretical and experimental results show that the material is mainly removed by the interfacial tribo-chemical effect between polishing particle and quartz glass during CMP process. The depth of a single particle embedding into the quartz glass is at molecular scale, and the superficial molecules of quartz glass are removed by chemical reactions because of enough energy obtained. The material removal rate of quartz glass during CMP process is determined by the polishing pressure, the chemical reagents and its concentration, and the relative movement speed between the quartz glass workpiece and the polishing pad.