A method of repairing a semiconductor chip containing copper is taught, whereby copper is selectively removed from the chip. The method involves processing the chip inside a chamber in which the chip is exposed to various gases and an energy source, such as a focused ion beam. To the extent the chip may have non-copper materials, such as nitride and oxide layers, on top of the copper that is to be removed, those non-copper materials will first be selectively removed. Such removal typically results in a hole (a so-called "elevator shaft") leading to the copper that is to be removed. Next, the method teaches the introduction of a combination of nitrogen and oxygen into the chamber and the directing of the ion beam at the spot where the copper is to be removed. In this manner, the copper on the chip is cleanly and reliably removed, without causing damage to the processing chamber.