Solid-state nanopores fabricated by a high-intensity electron beam in ceramic membranes can be fine-tuned on three-dimensional geometry and composition by choice of materials and beam sculpting conditions. For similar beam conditions, 8 nm diameter nanopores fabricated in membranes containing SiO(2) show large depletion areas (70 nm in radius) with small sidewall angles (55 degrees ), whereas those made in SiN membranes show small depletion areas (40 nm) with larger sidewall angles (75 degrees ). Three-dimensional electron tomograms of nanopores fabricated in a SiO(2)/SiN/SiO(2) membrane show a biconical shape with symmetric top and bottom and indicate a mixing of SiN and SiO(2) layers up to 30 nm from the edge of nanopore, with Si-rich particles throughout the membrane. Electron-energy-loss spectroscopy (EELS) reveals that the oxygen/nitrogen ratio near the pore depends on the beam sculpting conditions.