*

We report 3D imaging and manipulation of individual Se vacancies in PdSe₂ using a STM. By imaging the characteristic charge rings of defects arising from a tip-induced band bending effect, we first determine the lateral and depth location of V_Se precisely in the 3D lattice. We then use a STM tip as a movable electrostatic gate to manipulate V_Se by reversibly switching the charge states of defects between neutral and negative states. We find a slightly higher bias voltage (~2.0 V) can trigger vacancy migrations, which allows us to demonstrate both direct “writing” and “erasing” of atomic defects from a particular lattice site in PdSe₂. The results are corroborated by first-principles calculations that reveal the formation energy and diffusion barriers of Se vacancies in PdSe₂. This work opens an opportunity for defect engineering at the atomic level to achieve controlled phase transformations, or on-demand switchable states for such as neuromorphic computing and quantum bits.