Multilayer porous membranes and methods for fabricating the membranes may have applications in filtration, separation, and nanomanufacturing. The layers of the membrane may be selected based on different physiochemical properties, such as ionization rate and/or etch rate. The pores may be formed by high energy particle bombardment and chemical etching. In some embodiments, the multilayer porous membrane may be utilized to form complex nanostructures by selecting different materials for the layers based on physiochemical properties, layer thickness, stacking sequence, and/or varying the pore generation process.