Solid-state single photon sources (SPSs) with narrow linewidth play an important role in many leading quantum technologies. Within the wide range of SPSs studied to date, single fluorescent molecules hosted in organic crystals stand out as bright, photostable SPSs with lifetime-limited optical resonance at cryogenic temperatures. Furthermore, recent results have demonstrated that photostability and narrow linewidths are still observed from single molecules hosted in organic nanocrystals, which paves the way for their integration with photonic circuitry. Polymers offer a compatible matrix for embedding nanocrystals and provide a versatile yet low-cost approach for making nanophotonic structures on chip which guide light and enhance coupling to nanoscale emitters. Here, we present a deterministic nanostructuring technique based on electron-beam lithography for shaping polymers with embedded single molecules. Our approach provides a direct mean of structuring the nanoscale environment of narrow linewidth emitters while preserving their emission properties.