The present invention provides a method of fabricating an imprint mold for molding a structure. The method includes directing a first and a second flux for forming a first material and a second material, respectively, to a substrate to form a layered structure having alternating layers of the first and the second material. The method also includes controlling a thickness of the first and the second layers by controlling the first and the second flux and cleaving the layered structure to form a cleavage face in which sections of the layers are exposed. The method further includes etching the exposed sections of the layers using a etch procedure that predominantly etches one of the first and the second materials to form the mold having an imprinting surface with at least one indentation for molding the structure. At least one of the fluxes is controlled so that at least one of the layers has a thickness that varies along a portion of a length of the at least one layer.