Provided are a combined laser and a charged particle beam system. A pulsed laser enables milling of a sample at material removal rates several orders of magnitude larger than possible for a focused ion beam. In some embodiments, a scanning electron microscope enables high resolution imaging of the sample during laser processing. In some embodiments, a focused ion beam enables more precise milling of the sample. A method and structure for deactivating the imaging detectors during laser milling enables the removal of imaging artifacts arising from saturation of the detector due to a plasma plume generated by the laser beam. In some embodiments, two types of detectors are employed: type-1 detectors provide high gain imaging during scanning of the sample with an electron or ion beam, while type-2 detectors enable lower gain imaging and endpoint detection during laser milling.