Molecular dynamics (MD) simulations have become a pivotal tool in the nanofabrication of semiconductor materials, a key area of contemporary semiconductor process research. This methodology has not only facilitated the exploration and optimization of semiconductor materials but has also significantly contributed to enhancing the performance of semiconductor devices by providing a deep understanding of their intrinsic properties. This paper systematically analyzes the methodologies employed in the nanofabrication of semiconductor materials, with a focus on elucidating the mechanical mechanisms and microstructural changes that occur during processing. We introduce and evaluate simulation models for innovative processing techniques such as surface texture, ion implantation, laser-assisted machining, and vibration-assisted machining. These methods demonstrate significant potential for improving processing efficiency and quality. Additionally, this article addresses the challenges in model optimization, including the refinement of potential functions, reaction force fields, chemical reaction prediction, and the development of advanced equipment. Finally, we outline future research directions, emphasizing the continued evolution and application of MD simulations in semiconductor material processing.