<p>Molybdenum disulfide (MoS₂), as a representative two-dimensional (2D) transition metal dichalcogenide, has attracted significant interest for next-generation electronic and optoelectronic devices. However, conventional lithography and etching processes often involve harsh chemicals or plasma treatments that introduce defects and residues, thereby limiting the reliable fabrication of MoS₂-based devices. Here, we demonstrate a two-step scanning probe lithography approach for the controlled etching of mechanically exfoliated MoS₂ flakes onto a silicon substrate. Contact mode atomic force microscopy (AFM) with a diamond-coated tip was used to perform mechanical etching under high-force conditions. The debris generated from the etching process was effectively removed by the subsequent cleaning step, which employed a mild-force contact mode operation. By this careful two-step etching process, a reliable contamination-free etching of a 2D MoS₂ flake was successfully carried out. Additionally, the contaminated diamond-coated AFM tip, which can be damaged during repeated etching processes, can be repaired with a simple oxygen plasma treatment. This approach can be applied to other 2D materials, including graphene, and provides a new direction for the nanofabrication of 2D materials in next-generation electronic devices.</p>