Multi-component organic molecular films have seen increasing applications in photovoltaic technologies and other organic electronic applications. These applications have been based upon assumptions regarding film structure and electronic properties. This thesis provides an increased understanding of factors that control structure in binary molecular films and begins to establish structure-electronic property relations. In this thesis, three technologically relevant "donor-acceptor" systems are studied with variable temperature STM/STS: pentacene (Pn):C60, zinc phthalocyanine (ZnPc): C60 and ZnPc: perfluorinated zinc phthalocyanine (F16ZnPc). These three model systems provide a systematic exploration of the impact of molecular shape and molecular band offset on morphology-electronic relations in thin film heterostructures.

For Pn:C60, I show how domain size and architecture are controlled by composition and film processing conditions. Sequential deposition of pentacene, followed by C60, yields films that range from nanophase-separated, to co-crystalline phases, to a templated structure. These distinct structures are selectively produced from distinct pentacene phases which are controlled via pentacene coverage.

For the ZnPc:C60 system, the shape of ZnPc and the lattice mismatch between ZnPc and C60 are quite different from the Pn:C60 films. Nonetheless, ZnPc:C60 films also yield chemical morphologies that can be similarly controlled from phase separated, to co-crystalline phases, to templated structures. In both of these binary films, I exploit relative differences in the component cohesive energies to control phase selection. In bilayer films of both systems, a common structural element of stress-induced defects is also observed.

In ZnPc:F16ZnPc, I explore two components with similar shapes and cohesive energies while retaining molecular band offsets comparable to Pn:C60. In this shape-matched system, a checkerboard ZnPc:F16ZnPc arrangement stabilized by hydrogen bonds readily forms. This supramolecular structure introduces a new hybridization state close to the Fermi Level, yielding electronic properties distinct from the component phases.

Through investigations of these three model systems, I have developed an understanding the control of chemical morphology along the donor-acceptor interface and the way this morphology influences electronic transport.