To offer a microstructure fabrication apparatus capable of realizing MEMS and a Rugate Filter excellent in performance characteristics by patterning a thick functional material film in high aspect ratio with a simple and practical manufacturing method. A Si layer is employed for a mask pattern. The advantages of the Si layer are withstood a process conducted at high temperature for forming a PZT layer, which is the functional material layer, patterned in high aspect ratio, and achieves excellent process consistency for the whole manufacturing processes of the microfabrication. A trench or a gap is formed with the mask pattern deeper than the desired PZT layer. The PZT layer, or functional material layer (films) is formed on the whole surface including the bottom of the concave part of the mask pattern. The PZT layer deposited on the mask pattern is removed with the mask pattern itself, and selectively remains the pattern of the PZT layer, thereby obtaining a pattern of the desired functional material layer.