A method for performing milling and imaging in a focused ion beam (FIB) system employing an inductively-coupled plasma ion source, wherein two sets of FIB system operating parameters are utilized: a first set representing optimized parameters for operating the FIB system in a milling mode, and a second set representing optimized parameters for operating in an imaging mode. These operating parameters may comprise the gas pressure in the ICP source, the RF power to the ICP source, the ion extraction voltage, and in some embodiments, various parameters within the FIB system ion column, including lens voltages and the beam-defining aperture diameter. An optimized milling process provides a maximum milling rate for bulk (low spatial resolution) rapid material removal from the surface of a substrate. An optimized imaging process provides minimized material removal and higher spatial resolutions for improved imaging of the substrate area being milled.