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Abstract Controlled fabrication of nanopores in 2D materials offer the means to create robust membranes needed for ion transport and nanofiltration. Techniques for creating nanopores have relied upon either plasma etching or direct irradiation; however, aberration‐corrected scanning transmission electron microscopy (STEM) offers the advantage of combining a sub‐Å sized electron beam for atomic manipulation along with atomic resolution imaging. Here, a method for automated nanopore fabrication is utilized with real‐time atomic visualization to enhance the mechanistic understanding of beam‐induced transformations. Additionally, an electron beam simulation technique, Electron‐Beam Simulator (E‐BeamSim) is developed to observe the atomic movements and interactions resulting from electron beam irradiation. Using the MXene Ti₃C₂T_x, the influence of temperature on nanopore fabrication is explored by tracking atomic transformations and find that at room temperature the electron beam irradiation induces random displacement and results in titanium pileups at the nanopore edge, which is confirmed by E‐BeamSim. At elevated temperatures, after removal of the surface functional groups and with the increased mobility of atoms results in atomic transformations that lead to the selective removal of atoms layer by layer. This work can lead to the development of defect engineering techniques within functionalized MXene layers and other 2D materials.