In a method for manufacturing the functional element, a protective film covering an underlayer, a patterned multilayer film, and a patterned cap layer are formed, and the underlayer is then processed without newly forming a resist. Thereby, an electrode can be formed in steps less than ever before. Since the protective film formed on the patterned multilayer film and the patterned cap layer is used as a mask, the problem of the misregistration can be prevented.