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Two-dimensional materials such as layered transition-metal dichalcogenides (TMDs) are ideal platforms for studying defect behaviors, an essential step towards defect engineering for novel material functions. Here, we image the 3D lattice locations of selenium-vacancy V_{Se} defects and manipulate them using a scanning tunneling microscope (STM) near the surface of PdSe_{2}, a recently discovered pentagonal layered TMD. The V_{Se} show a characterisitc charging ring in a spatially resolved conductance map, based on which we can determine its subsurface lattice location precisely. Using the STM tip, not only can we reversibly switch the defect states between charge neutral and charge negative, but also trigger migrations of V_{Se} defects. This allows a demonstration of direct "writing" and "erasing" of atomic defects and tracing the diffusion pathways. First-principles calculations reveal a small diffusion barrier of V_{Se} in PdSe_{2}, which is much lower than S vacancy in MoS_{2} or an O vacancy in TiO_{2}. This finding opens an opportunity of defect engineering in PdSe_{2} for such as controlled phase transformations and resistive-switching memory device application.