We studied the first-order diffractedmoiré fringes of transparent multilayered structures comprised of irregularly deformed periodic patterns. By a comparison study of the diffractedmoiré fringe pattern and detailed microscopy of the structure, we show that the diffractedmoiré fringe can be used as a nondestructive tool to analyze the alignment of multilayered structures. We demonstrate the alignment method for the case of layer-by-layer microstructures using soft lithography. The alignment method yields high contrast of fringes even when the materials being aligned have very weak contrasts. The imaging method of diffractedmoiré fringes is a versatile visual tool for the microfabrication of transparent deformable microstructures in layer-by-layer fashion.