A method and system of manual windowing within a displayed image is disclosed, which include specifying different windows within a displayed image, assigning tags to different windows, assigning processing channels to the windows, processing the different windows on the basis of the assigned tags and assembling the different windows. A scanner is disclosed which sends image data to a manual window construction module which specifies a plurality of windows within a displayed image and which assigns specific tags to each one of the plurality of windows. According to various exemplary embodiments, the windows are processed separately and re-assembled by a processor.