Disclosed is a method for processing a three-dimensional structure having a fine three-dimensional shape and a smooth surface is disclosed in which the three-dimensional structure is usable for an optical device.The process method comprises the steps of depositing a thin layer for absorption of laser light on a flat substrate; depositing a transparent layer on the thin layer for absorption of laser light; and irradiating a process laser light, passing through the transparent layer; in which pulse injection energy of the process laser light is set to be the same as or smaller than the maximum pulse injection energy capable of exposing a surface of the thin layer in front in the incident direction of the process laser light, and to be set the same as or greater than the minimum pulse injection energy capable of removing the transparent layer in rear in the incident direction of the process laser light.