A comparative study of the self-assembly at a variety of surfaces of a dithiophene rotaxane 1 subset of beta-CD and its corresponding dumbbell, 1, by means of atomic force microscopy (AFM) imaging and scanning tunneling microscopy (STM) imaging on the micrometer and nanometer scale, respectively. The dumbbell is found to have a greater propensity to form ordered supramolecular assemblies, as a result of pi-pi interactions between dithiophenes belonging to adjacent molecules, which are hindered in the rotaxane. The fine molecular structure determined by STM was compared to that obtained by molecular modelling. The optical properties of both rotaxane and dumbbell in the solid state were investigated by steady-state and time-resolved photoluminescence (PL) experiments on spin-cast films and diluted solutions. The comparison between the optical features of the threaded and unthreaded systems reveals an effective role of encapsulation in reducing aggregation and exciton migration for the rotaxanes with respect to the dumbbells, thus leading to higher PL quantum efficiency and preserved single-molecule photophysics for longer times after excitation in the threaded oligomers.