A self-assembly nanopatterning method for epitaxial-CoSi 2 layers has been developed and investigated. It is based on anisotropic diffusion of Co/Si atoms in a stress field during rapid thermal oxidation. The stress field is generated by a patterned trench mask consisting of 20 nm SiO 2 and 300 nm Si 3N 4. Single-crystalline CoSi 2 layers with a thickness of 20 nm grown by molecular beam allotaxy (MBA) on Si(100) substrates were patterned using this technique. Uniform gaps or uniform CoSi 2 wires with a feature size of 80 nm have been fabricated by using different stress fields which are created by different trench widths.