Methods and systems for accurately locating buried defects previously detected by an inspection system are described herein. A physical mark is made on the surface of a wafer near a buried defect detected by an inspection system. In addition, the inspection system accurately measures the distance between the detected defect and the physical mark in at least two dimensions. The wafer, an indication of the nominal location of the mark, and an indication of the distance between the detected defect and the mark are transferred to a material removal tool. The material removal tool (e.g., a focused ion beam (FIB) machining tool) removes material from the surface of the wafer above the buried defect until the buried defect is made visible to an electron-beam based measurement system. The electron-beam based measurement system is subsequently employed to further analyze the defect.