Nanofabrication techniques for superconducting qubits rely on resist-based masks patterned by electron-beam or optical lithography. We have developed an alternative nanofabrication technique based on free-standing silicon shadow masks fabricated from silicon-on-insulator wafers. These silicon shadow masks not only eliminate organic residues associated with resist-based lithography, but also provide a pathway to better understand and control surface-dielectric losses in superconducting qubits by decoupling mask fabrication from substrate preparation. We have successfully fabricated aluminum 3D transmon superconducting qubits with these shadow masks, and demonstrated energy relaxation times on par with state-of-the-art values.