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Binary optical elements (BOE) tend to be used frequently in optical equipment because aspherical type BOE is easy to fabricate and the BOE can easily correct chromatic aberration. What makes this technology attractive to industry is that the BOE can be fabricated precisely by the semiconductor micro fabrication technique. However when it is used for more precise optics e.g. semiconductor exposure equipment, more precise BOE are necessary. In some manufacturing processes, we have confirmed that the alignment error between masks is the dominant factor to decrease diffraction efficiency by optical simulation. To study this problem, we have produced a BOE using a novel self-alignment method we have devised, then compared it to a BOE which has being made by a conventional method.