A method for aligning optical layers of a multi-layer display includes displaying a dark screen image on each of a plurality of transmissive pixel arrays separated from each other by spacing regions. The transmissive pixel arrays are disposed on a display layer of the multi-layer display. The display layer is illuminated with a plurality of illumination sources of an illumination layer disposed behind the display layer. Each of the illumination sources corresponds to one of the transmissive pixel arrays to illuminate the corresponding one of the transmissive pixel arrays. An illumination pattern is cast onto a screen layer disposed in front of the display layer. The illumination pattern includes bright regions due to overlapping illumination cast from adjacent ones of the transmissive pixel arrays. The bright regions of the illumination pattern cast onto the screen layer are analyzed to identify misalignments between the display layer and the illumination layer.