A new class of microstructures, such as the opposed gate–source transistor, requires the careful alignment of submicron features on two opposite surfaces of a substrate. Concepts for self‐aligned methods for accomplishing dual‐surface lithography have been explored for the first time. Self‐alignment is based on the integration of the exposure mask into the microstructure and subsequent exposure through the substrate. Electrons, ions, and x rays have been explored for exposing lines as narrow as 200 nm. Both theoretical Monte Carlo results and experimental data on fabricated structures are given. Self‐aligned dual‐surface lines with a width of 200 nm have been demonstrated across a 3‐μm‐thick silicon membrane. Ion, electron, and x‐ray exposure through the substrate limits the thickness of the membrane to about 100 nm, 1 μm, and 10 μm, respectively for reasonable particle energies and submicron resolution.