Abstract We have integrated one-dimensional organic structures into semiconductor/insulator nanostructures by controlled self-assembly. Stepped Si(111) surfaces with self-organized CaF 1/CaF 2 stripe patterns serve as mask for selective adsorption of 3,10-di(propyl)perylene. These molecules adsorb preferentially on CaF 1 nanostripes, rather than on CaF 2. This property is used to fabricate large assemblies of parallel, equidistant stripes 1–15 nm wide. We discuss the selectivity in terms of a mechanism where the HOMO and LUMO of the molecule interact with the valence band and conduction band of CaF 1 and CaF 2.