Recently, plasma etching has become one of the most promising polishing methods due to its low cost and environmental friendliness. In this study, the mechanism and parametric influence of plasma etching were investigated using ReaxFF-based molecular dynamics (RBMD) simulation, allowing the characterization of the process of F atom etching of monocrystalline silicon and the removal of subsurface defects from an atomic perspective. We simulated the process of F-atom etching and the mechanism of F-atom removal of the subsurface damage of single-crystalline silicon. The simulation results indicate that SiF4 generated by monocrystalline silicon under the action of F atoms gradually generated SiF5- groups and detached from the substrate as the reaction time increases. Simultaneously, under the action of F atoms, Si atoms gradually filled the subsurface defects, achieving damage removal. In addition, the incident angle can be increased in the plasma polishing process to reduce the thickness of the amorphous deformation layer and improve the surface quality.