With the great success of graphene, two-dimensional (2D) materials, thanks to their fascinating electronic and optoelectronic properties, have aroused extensive attention among the scientific community. Broad research efforts have proven the enormous potential of 2D materials in optoelectronics, electrochemistry, spintronics, energy storage, catalysis, biomedicine, and many other fields. Driven by the promising applications of 2D materials, there has been an emerging trend toward nanofabricating 2D materials with customized parameters, which are essential for tailor-making controllable artificial nanostructures used in building sophisticated 2D material systems. As the most commonly used solid probe lithography technique, atomic force microscopy (AFM) integrates visualization and multi-mode fabrication within one system, demonstrating its superior capability in the nanofabrication of 2D materials. In view of this, in this review article, we offer a brief introduction to how AFM nanofabrication works and the classification of AFM nanofabrication techniques by the tip-sample surface interaction. Following that, we discuss the results of 2D material nanofabrication by mechanical, thermal, electrical, and other AFM techniques in which external stimulations are applied on special AFM probes.