Variations in charged-particle-beam (CPB) source location are determined by scanning an alignment aperture that is fixed with respect to a beam defining aperture in a CPB, particularly at edges of a defocused CPB illumination disk. The alignment aperture is operable to transmit a CPB portion to a secondary emission surface that produces secondary emission directed to a scintillator element. Scintillation light produced in response is directed out of a vacuum enclosure associated with the CPB via a light guide to an external photodetection system.