Synthesis and processing techniques have now been established for obtaining high quality monodisperse nanocrystals of various metallic and semiconducting materials, fullerenes of distinct properties, single- and multi-wall carbon nanotubes, polymeric dendrimers with tailored functionalities, as well as other nanophase constructs. The next key step towards novel applications of nanostructured materials concerns their positioning, arrangement, and connection into functional networks without mutual aggregation. In this review, we highlight the recent progress of using anthraceneand pyrene-based self-assembling molecules with tunable energetic (pi-pi interactions, hydrogen bonding, dipole-dipole interactions) and variable geometries to create stable, highly ordered, and rigid self-assembled monolayer (SAM) templates with adjustable superlattices on crystalline substrates. Based on aromatic SAM templates, stable and highly ordered self-assembled structures of optoelectronically active C-60 have been obtained and shown to exhibit desirable electrical and optoelectronic properties, such as nonlinear transporting effect for molecular electronics and efficient photocurrent generation for mimicking photosynthesis in nature. By using genetically engineered polypeptides with surface recognition for specific inorganics, selective integration of nanoparticles onto aromatic SAM templates have also been realized. Through a combination of spatially confined surface chemical reaction and microcontact printing, sub-micron arrays of peptide-organic hybrid conjugates were successfully generated to serve as templates to achieve the patterned assembly of nanoparticles.