In many laser processing applications, galvanometer scanners are integrated to a larger system that creates external disturbances to the actual laser-material interaction. To reject such disturbance with feedback-based control schemes, the sampling of the output needs to be fast enough to capture all major frequency components of the disturbance. In some applications, however, the sensor’s sampling speed is limited, such that the disturbance is beyond the sampler’s Nyquist frequency. This paper introduces a multi-rate control scheme to fully reject narrow-band beyond-Nyquist disturbances in galvanometer scanner systems. The proposed algorithm consists of a special bandpass filter with tailored frequency response, and a model-based predictor that reconstructs signals from limited sensor data. Verification of this algorithm is conducted by both simulated and experimental results on a commercial galvanometer scanner testbed.