The self-assembly behaviour, structure, and consequently the electronic properties of electroactive organic molecules can differ significantly from those of the bulk material when confined to thin films. Here we have examined the self-organised in-plane and out-of-plane structures of aniline oligomers in thin films using surface-sensitive grazing-incidence X-ray scattering (GIXS). Thin films of the aniline tetramer (TANI) and octamer (OANI) were prepared both in their native emeraldine base (EB) oxidation state and in the doped emeraldine salt (ES) state (combined with the acid surfactant bis(ethyl hexyl)phosphate (BEHP)), using a simple drop-casting and solvent annealing process. It was found that the presence of the acid surfactant induced self-organisation into highly ordered structures. The details of these structures, such as the morphology, orientation relative to the underlying substrate and the degree of orientation were found to depend on the molecular architecture of the oligomer. The BEHP-doped TANI system formed a highly oriented hexagonal unit cell (lattice parameters: a = b = 2.53 nm, c = 2.91 nm, γ = 120°), whereas the BEHP-doped OANI complex adopted a randomly oriented lamellar structure (d-spacing = 2.25 nm). Such detailed structural information reveals that the self-assembly behaviour and the packing of oligomer–BEHP complexes, when confined to thin films, are indeed different to that of the bulk phase materials. Furthermore, the molecular architecture of the oligomers directly influenced the structural changes of the doped films in response to in situ thermal treatment. These results demonstrate that through a simple processing route the morphology of electroactive oligomer films can be tailored by molecular design. These findings are important to future applications where thin film structure is a crucial consideration for device function and performance.