Self-assembled supramolecular structures such as optical wires, films and 2D slabs offer a new generation of electronic and optical devices. In particular, self-assembled porphyrin devices, including those integrated onto silica and silicon platforms, open new opportunities in photonic applications spanning molecular biosensing, photovoltaics and telecommunications. All reports to date, however, largely highlight the potential but have not established a clear pathway to the actual implementation of more complex device prototypes. In this paper, we propose and demonstrate the use of a focused ion beam (FIB) to process and fabricate devices in porphyrin-based supramolecular structures. These self-assembled structures have an initial root mean squared (rms) values for surface roughness of <0.5 nm as measured by atomic force microscopy. Under appropriate FIB processing and cutting conditions, the rms value for surface roughness falls to <0.4 nm, comparable with some of the best optical flatnesses obtained within, for example, structured optical fibres and integrated optical waveguides. The milling rate of the porphyrin structures was estimated to be ~70% of that of silica. The versatility of a FIB as a tool for rapid processing and fabricating 1D and 2D photonic waveguide structures within supramolecular self-assembled platforms is demonstrated by fabricating a 2D coupler, setting the groundwork for true optical device engineering and integration using these new organic systems.