Methods and apparatus for integrated circuit diagnosis, characterization or modification using a focused ion beam. A method for editing an integrated circuit includes acquiring an image of structures of an integrated circuit by applying a focused ion beam to an outer surface of the integrated circuit to visualize structures beneath the outer surface of the integrated circuit. The method includes using the image to find a location of a circuit element in the integrated circuit and then performing one or more editing operations on the circuit element by applying a focused ion beam to the location found.