A biochip substrate capable of realizing the high detection accuracy by restricting a nonspecific adsorption or bonding of a substance to be detected, when used for a detection or analysis of protein, nucleic acids and the like. The variable aperture device is configured to adjust an ion beam width in a direction perpendicular to an ion beam focusing direction at the focus point in order to control an implanting beam current. The photoresist is exposed without a mask at a dose that allows the developer to thin the photoresist to a recessed depth within the holes.