Since the 1985 discovery of C60, fullerenes have emerged as key nanoelectronic components and promising biomedical probes. Understanding how to direct-and switch-the packing arrangements of fullerenes and their chemical derivatives at interfaces is important for advanced applications. In this thesis work, we explore structural motifs that can be achieved in films of the fullerene derivatives, phenyl-C61-butyric-acid methyl ester (C60-PCBM) and phenyl-C71-butyric-acid methyl ester (C70-PCBM), and metal phthalocyanines (ZnPc and tetranitro-ZnPc(TN-ZnPc)), at neat and chemically-modified Au (111) and Ag (111) substrates. On low-index metals, we observe how molecular ordering in C60-PCBM and C70-PCBM monolayers is frustrated by anisotropic fullerene-fullerene interactions. Transition to crystalline (2D hexagonal) fullerene arrangements is highly activated and dependent on local density. Molecular electrostatics provides a useful tool to rationalize observed packing arrangements in PCBM films and the barriers for nanocrystallization. Additionally, we describe how molecular electrostatics drive vertical phase separation in binary PCBM-ZnPc mixtures. Finally, we report a primary study of supramolecule deposition, structures and stabilization on Ag (111).