This dissertation is concerned with the materials properties of conjugated molecules and their application in bulk heterojunction (BHJ) type solar cells with particular attention paid to the role of processing in determining morphology and device performance. Utilizing alternating electron rich and electron deficient moieties in the conjugated backbone results in tunable energy levels allowing molecules to be tailored to achieve desired optoelectronic characteristics. Two high performance materials in particular are studied in detail with respect to their physical and electronic properties. Specifically, high-resolution transmission electron microscopy, atomic force microscopy, UV-viable absorption spectroscopy and x-ray diffraction are used to examine the BHJ nanostructure in conjunction with current voltage measurements to elucidate structure property relationships. A series of molecules designed for specific goals such as improved absorption and electronics are also each briefly described. Though none of these materials give high efficiencies in BHJ solar cells compared with the first two materials, these smaller studies help demonstrate the intricacies of controlling morphology and how it can affect device performance.