An improved method and apparatus for shutting down and restoring an ion beam in an ion beam system. Preferred embodiments provide a system for improved power control of a focused ion beam source, which utilizes an automatic detection of when a charged particle beam system is idle (the beam itself is not in use) and then automatically reducing the beam current to a degree where little or no ion milling occurs at any aperture plane in the ion column. Preferred embodiments include a controller operable to modify voltage to an extractor electrode and/or to reduce voltage to a source electrode when idle state of an ion source of the charged particle beam system is detected.