A method of manufacturing a structure with pores which are formed by anodic oxidation and whose layout, pitch, position, direction, shape and the like can be controlled. The method includes the steps of: disposing a lamination film on a substrate, the lamination film being made of insulating layers and a layer to be anodically oxidized and containing aluminum as a main composition; and performing anodic oxidation starting from an end surface of the lamination film to form a plurality of pores having an axis substantially parallel to a surface of the substrate, wherein the layer to be anodically oxidized is sandwiched between the insulating layers, and a projected pattern substantially parallel to the axis of the pore is formed on at least one of the insulating layers at positions between the pores.