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Here we demonstrate control over the charge state and layer position of individual defects in the layered semiconductor, 2H-MoTe₂. Pristine surfaces were revealed at room temperature in ultrahigh vacuum by cleaving the top few layers from the crystal. STM images and spectroscopy were performed with a cut PtIr tip at 9K. Two classes of native defects were observed in large area STM images, appearing in both near-surface and sub surface layers with progressively fainter contrast. One class of defect images as a bright protrusion with a nm-scale fall-off in STM topography, indicative of band bending associated with a charged defect. Spectroscopic imaging reveals a ring-shaped feature associated with these defects, consistent with tip-induced ionization between two defect charge states. Consistent with studies in other semiconductor systems, the rings depend on the STM imaging conditions and tip apex. We find that subsurface defects exhibit discrete increases in apparent height following large positive voltage pulses, suggesting migration between layers near the surface. We compare with DFT calculations to identify these defects and estimate the energy barriers for inter-layer migration.