In one embodiment a method of etching a substrate includes directing a first ion beam to the substrate through an extraction plate of a processing apparatus using a first set of control settings of the processing apparatus. The method may further include detecting a signal from the substrate that indicates a change in material being etched by the first ion beam from a first material to a second material, adjusting control settings of the processing apparatus to a second set of control settings different from the first set of control settings based on the second material, and directing a second ion beam to the substrate through the extraction plate using the second set of control settings.