Two-dimensional scanning array microscope system, which has fields of view of individual objectives overlapping at the object, produces a composite image of the object that is devoid of optical distortions caused by such overlapping. Method for processing imaging data with the system includes precise identification of detector pixels corresponding to different portions of multiple image swaths projected on the detector by the system during the scan of the object, and, based on such identification, allocating or assigning of detector pixels that receive light from the object through more than one objective to only one of objectives, thereby correcting imaging data received in real time to remove a portion of data corresponding to image overlaps.