In this work the electronic and geometric structure of interfaces of organic thin films with metallic substrates is studied using the orbital tomography technique. Orbital tomography combines angle resolved photoemission spectroscopy experiments with calculations within the framework of density functional theory and is based on the approximation of the final state by a simple plane wave in the theoretical description of the photoemission process. With this approximation, the experimental data is interpreted as the Fourier transform of the initial state molecular orbitals under investigation. With the help of orbital tomography, the azimuthal alignment of copper-II-phthalocyanine on Au(110) as well as the level alignment of PTCDA and copper-II-phthalocyanine co-adsorbed on Ag(111) is unambiguously determined. In order to include effects arising from intermolecular band dispersion or from the interaction of he molecules with the substrate, extended systems are included in the simulation of angle resolved photoemission intensity maps. Thereby the experimental photoemission intensity of pentacene on Cu(110) is found to behave like that of the isolated molecule modulated by the band dispersion due to intermolecular interactions. The orbital level alignment of the bulk phase of quinacridone is obtained in excellent agreement with photoemission experiments using an optimally-tuned screened range-separated hybrid functional. Furthermore, images of individual molecular orbitals are obtained with the only assumption of the wave function to be confined to a region, defined by the spatial extend of the molecule. Using this assumption, an iterative procedure, commonly applied in x-ray diffraction experiments, allows for the recovery of the phase information, that is lost in the experiment. The so obtained orbitals orbitals are found to be in excellent agreement with calculated one electron orbitals obtained within density functional theory.