We present an innovative fabrication method for solid-state nanoporous membranes based on the casting of sacrificial silicon nanostructures. The process allows the individual definition of geometry and placement of each nanopore through e-beam lithography and is compatible with a wide range of materials without the need to adapt the process to the materials used. We demonstrate the fabrication of membranes integrating high aspect-ratio nanopores with critical dimensions as small as 30 nm, 1.2 μm in length, with round or elongated shapes, and made of silicon dioxide or amorphous carbon. The capability to engineer nanoporous membranes made of a variety of materials and with tailored designs will lead to new applications in the field of electrochemical sensing, flow modulation, or the chemical functionalization of nanopores.