A method for rapid switching between operating modes with differing beam currents in a charged particle system is disclosed. Many FIB milling applications require precise positioning of a milled pattern within a region of interest (RoI). This may be accomplished by using fiducial marks near the RoI, wherein the FIB is periodically deflected to image these marks during FIB milling. Any drift of the beam relative to the RoI can then be measured and compensated for, enabling more precise positioning of the FIB milling beam. It is often advantageous to use a lower current FIB for imaging since this may enable higher spatial resolution in the image of the marks. For faster FIB milling, a larger beam current is desired. Thus, for optimization of the FIB milling process, a method for rapidly switching between high and low current operating modes is desirable.