The invention is describes the design, materials selection and fabrication techniques to produce multilayered membranes with individually controllable pores in constituent layers. Current available nanoporous membranes are all single layers with uniform pore diameters. Produced multilayer membranes can have applications in filtration, separation, and nanomanufacturing. This patent covers the materials selection based on their different physiochemical properties, the method to combine different layers into stackable multi layers, stacking sequence and layer thickness design; and the process of nanopores generation. High energy particle bombardment will be used to generate damage tracks in multilayers. Nanopores will be formed by controlled chemical etching of the nuclear track damages in individual constituent layers.