Systems and methods for irradiating a sample with a charged-particle beam are disclosed. The charged-particle beam system may comprise a stage configured to hold a sample and is movable in at least one of X-Y-Z axes. The charged-particle beam system may further comprise a position sensing system to determine a lateral and vertical displacement of the stage, and a beam deflection controller configured to apply a first signal to deflect a primary charged-particle beam incident on the sample to at least partly compensate for the lateral displacement, and to apply a second signal to adjust a focus of the deflected charged-particle beam incident on the sample to at least partly compensate for the vertical displacement of the stage. The first and second signals may comprise an electrical signal having a high bandwidth in a range of 10 kHz to 50 kHz, and 50 kHz to 200 kHz, respectively.