The demand for polished silicon wafers has increased significantly in recent years to cater to the development of the semiconductor industry. For example, polished silicon wafer has direct applications in integrated circuits, radio frequency amplifiers, micro-processors, micro-electromechanical systems, etc. To carry out mechanical polishing, lapping, grinding, or single-point diamond turning of silicon, diamond abrasives were extensively used before the implementation of chemo-mechanical polishing. During the diamond-based polishing, a few problems have already been identified, such as the formation of an amorphous phase, heat-affected zones, low material removal, etc. Some research work has also reported that nano-structured abrasives lead to a thin layer of the amorphous phase and a better material removal rate. In the same direction, a molecular dynamics simulation is carried out in this paper to investigate the mechanism of material removal from monocrystalline silicon during the diamond-abrasive-based polishing process. The present work is mainly focused on the dynamics of material removal phenomena near the abrasive particles at the nanometric scale by considering stress, lattice, cohesive energy, etc. This reveals that a higher value of indentation force results in surface buckling, which creates a zone of both compressive and tensile stresses, which increases the coordination number and forms β-silicon just ahead of the abrasive particle. This mechanism happens by developing a β-silicon phase on the surface with a thickness beyond a certain value of indentation force on the zone of compression. Buckling on this phase happens due to stress localisation in compression, as the flow stress of this phase is less than that of diamond cubic lattices. To avoid the mechanism of surface buckling and process silicon material on the surface, the indentation force needs to be maintained below a critical value. In the present case, it was found that the indentation force of less than or equal to 190 nN for the abrasive size of ϕ8 nm does the material removal by surface processing only without surface buckling. It was also found that surface processing helps to reduce the depth of the amorphous layer significantly without compromising the material removal rate or the generation of a wavy surface. Thus, the present mechanism will help in the polishing of silicon with minimum defects and reduce processing time for the final stage of polishing towards manufacturing ultra-smooth and planer surfaces.