The performance of devices based on small molecules depends on their molecular architecture and their two- and three-dimensional organisation into thin films. In this thesis scanning probe microscopy and density functional theory calculations are used to elucidate packing of poly(aniline) oligomers, oligo(aniline)s, into films formed by vacuum thermal evaporation and solution-processing. Thermal deposition of oligo(aniline)s under ultra-high vacuum conditions and subsequent study by scanning tunneling microscopy at various temperatures highlights two key issues with the preparation of oligo(aniline) thin films by this method. Firstly, the underlying copper substrate was shown to catalyse the fragmentation of oligo( aniline)s even at temperatures as low as 30 K. Secondly, upon an interfacial layer of fragmented molecules further disordered layers form, these layers are disordered due to presence of multiple isomeric forms of oligo(anilines). These two issues will prevent the preparation of high-quality oligo(aniline) thin films, and therefore limit the successful application of these molecules into devices. Computational studies of the isomerism of oligo(aniline)s undertaken by ab initio quantum calculations revealed a wealth of information about the gas-phase behaviour of these molecules. The energy barriers to cis/trans, syn/anti and ring rotation are extracted, as well as the kinetics of all these processes. Relatively low energetic barriers coupled with the small energy differences between isomers suggest that thin films of these molecules will be subject to conformational disorder than will inhibit their performance in applications. This led to the calculation of the molecular structures of ladder oligo( aniline )s. These were shown to be planar and rigid, and therefore offer attractive potential synthetic targets if the unique properties of oligo( aniline)s are to be exploited. Self-assembly of an amphiphilic oligo( aniline) into thin films by solution processing was investigated by tapping-mode atomic force microscopy and scanning tunneling microscopy. The driving forces for the formation of self-assembled thin films of oligo ( aniline)s are a delicate balance of non-covalent interactions. By taking a methodical approach, thin films of vertically or horizontally oriented oligo( aniline) molecules in their semi-conducting or conducting state could be formed by simple drop-casting. Important thin film properties are highly anisotropic, and the ability to control the orientation of molecules within a film is crucial for maximising device performances. Scanning tunneling microscopy of self-assembled monolayers of oligo(aniline)s reveals their surface structures, and offers the potential to manipulate them on a single molecule basis.