Methods and devices are disclosed for aligning a beam-propagation axis with the center of an aperture, especially an aperture configured to limit the aperture angle of the charged particle beam. In an exemplary method, an alignment-measurement aperture is provided at an imaging plane of a charged-particle-beam (CPB) optical system, and a beam detector is downstream of the alignment-measurement aperture. A scanning deflector is energized to cause the beam to be scanned in two dimensions, transverse to an optical axis, over the aperture. Meanwhile, the beam detector obtains an image of beam intensity in the two dimensions. In the image a maximum-intensity point is identified, corresponding to the propagation axis. Based on the two-dimensional image, the beam is deflected as required to align the propagation axis with the aperture center.