We studied the first-order diffracted moiré fringes of transparent multilayered structures comprised of irregularly deformed periodic patterns. By a comparison study of the diffracted moiré fringe pattern and detailed microscopy of the structure, we show that the diffracted moiré 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 diffracted moiré fringes is a versatile visual tool for the microfabrication of transparent deformable microstructures in layer-by-layer fashion.