Various methods and systems are provided for fabrication of nanoporous membranes. In one embodiment, among others, a system includes electrode pairs including substantially parallel electrodes, a controllable power supply to control the electrical potential of each of the electrode pairs, and a syringe to eject an electrically charged solution from a needle to form a nanofiber. The orientation of the nanofiber in a nanofiber layer is determined by the electrical potentials of the electrode pairs. In another embodiment, a method includes providing a nanoporous membrane including nanofiber layers between a transferor and a mainmold of a stamp-through-mold (STM) where adjacent nanofiber layers are approximately aligned in different directions. A patterned membrane is sheared from the nanoporous membrane using the transferor and the mainmold of the STM and transferred to a substrate.