Opto-electronically active organic molecules offer several advantages over traditionalsolid-state semiconductor materials in the fabrication of solar cells, including their low cost, light weight, and flexibility. Here, we present the results of combined SPM and DFT investigations of proposed molecular solar cell components, with the goal of developing a systematic understanding of the origin of specific properties to facilitate the enhancement of the efficiency and functionality of such devices. The molecules studied in this work include functionalized C60 molecules, which serve as electron acceptors in polymer based solar cells, as well as forming components of the block copolymers used as surfactants to control the separation of the donor and acceptor molecules into different phases. The interaction between these molecules and metallic substrates is also investigated.