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Abstract Manipulation and structural modifications of 2D materials for nanoelectronic and nanofluidic applications remain obstacles to their industrial‐scale implementation. Here, it is demonstrated that a 30 kV focused ion beam can be utilized to engineer defects and tailor the atomic, optoelectronic, and structural properties of monolayer transition metal dichalcogenides (TMDs). Aberration‐corrected scanning transmission electron microscopy is used to reveal the presence of defects with sizes from the single atom to 50 nm in molybdenum (MoS₂) and tungsten disulfide (WS₂) caused by irradiation doses from 10¹³to 10¹⁶ions cm⁻². Irradiated regions across millimeter‐length scales of multiple devices are sampled and analyzed at the atomic scale in order to obtain a quantitative picture of defect sizes and densities. Precise dose value calculations are also presented, which accurately capture the spatial distribution of defects in irradiated 2D materials. Changes in phononic and optoelectronic material properties are probed via Raman and photoluminescence spectroscopy. The dependence of defect properties on sample parameters such as underlying substrate and TMD material is also investigated. The results shown here lend the way to the fabrication and processing of TMD nanodevices.