We report an original iterative method for fabricating three-dimensional mesoporous structures by independently stacking multiple self-assembled block copolymer films supported by Si membranes. A first layer is formed on the substrate by a self-assembled PS-b-PMMA (polystyrene-block-poly(methyl methacrylate)) film. A porous, permeable Si membrane deposited on top of the first block copolymer film provides mechanical support, preventing pattern collapse during the wet developing used to selectively remove the PMMA component of the PS-b-PMMA film. A second, dense Si membrane is deposited to seal the porous membrane, resulting in an impermeable coating suspended atop the self-assembled mesoporous polystyrene structures. The process can then be iterated using the sealed membrane as the new substrate to support a subsequent self-assembled block copolymer film. This multilayer approach provides a flexible three-dimensional fabrication technique where, in each layer, pattern morphology, domain orientation and degree of ordering can be designed independently. Furthermore, the process is compatible with electron-beam directed assembly, used to achieve regular patterns with feature density multiplication at any level in the stack.