The surface of molybdenum disulfide (MoS₂) underwent oxygen plasma treatment to enhance its machinability and mitigate the tearing effects commonly associated with mechanical forces on 2D materials. This treatment led to the oxidation of the atoms on the top 1–3 layers of MoS₂, resulting in the formation of MoO₃ on the surface. During mechanical scanning probe lithography (m-SPL), only the surface oxide layer was uniformly removed, with material accumulation occurring predominantly on one side of the machined area. The resolution of the machining process was significantly enhanced via dynamic lithography while maintaining atomic-level smoothness in the machined area. Importantly, these techniques only removed the surface oxide layer, preserving the integrity of the underlying MoS₂ surface, which was pivotal in avoiding damage to the original material structure. This study provided valuable insights and practical guidance for the nanofabrication of transition metal dichalcogenides (TMDCs) nanodevices, demonstrating a method to finely tune the machining of these materials.