Systems and methods of imaging and repairing defects on and below the surface of an integrated circuit (IC) are described. The method may be used in areas as small as one micron in diameter, and may remove the topmost material in the small spot, repeating with various layers, until a desired depth is obtained. An energetic beam, such as an electron beam, is directed at a selected surface location. The surface has an added layer of a solid, fluid or gaseous reactive material, such as a directed stream of a fluorocarbon, and the energetic beam disassociates the reactive material in the region of the beam into radicals that chemically attack the surface. After the defect location is exposed, the method uses the energetic beam to etch undesired materials, and deposit various appropriate materials to fill gaps, and restore the IC to an operational condition.