A multi-beam metrology system includes an illumination source configured to generate a beam array, an illumination sub-system to direct the beam array to a sample at an array of measurement locations, an imaging sub-system to image the array of measurement locations as an array of imaged spots in a detection plane, and a detection assembly to generate detection signal channels associated with each of the imaged spots. The detection assembly includes an array of detection elements configured to receive the imaged spots with separate detection elements, and one or more position detectors to measure positions of the imaged spots in the detection plane. The detection assembly further generates feedback signals for the imaging sub-system based on the measured positions of the imaged spots to adjust the positions of one or more of the imaged spots in the detection plane to maintain alignment of the array of detection elements.