Promoting, structuring, or limiting adsorption of polyelectrolytes at interfaces is of importance in applications ranging from biomedical devices to nanoscale electronics. Routes for surface functionalization, particularly those capable of controlling the molecular conformation of adsorbates, are typically highly customized for the substrate and must therefore be redeveloped for each application. Here, we show that polymerized diacetylene striped phases with embedded 1 nm resolution functional patterns control polyelectrolyte adsorption on a crystalline inorganic surface (graphite) and can be easily transferred to elastomeric materials (here, poly(dimethylsiloxane), PDMS) to control adsorption on amorphous surfaces as well. We demonstrate that transferred functional poly(diacetylene) layers on PDMS can be designed to promote adsorption of polyelectrolytes or to limit protein adsorption, two common goals in controlling PDMS surface chemistry for biomedical applications.