Advances in lithography, electron optics, scanning probe microscopies, and time-resolved spectroscopies allow us to assemble and probe matter at the atomic level on femtosecond time scales. Nevertheless the capacity to utilize molecular systems in devices has not kept pace; many important technology platforms still require the ability to fabricate systems on molecular length scales using methods that are easily translated into large-area production. In the Ragan group, materials fabrication is designed to be compatible with large-scale manufacturing. Self-organization techniques using both atomic structure on crystal templates and localized chemical reactions on substrates are used in order to fabricate functional molecular scale systems with controllable atomic (molecular) structure. These include metal nanoarchitectures and biomolecular-metal hybrid systems. On molecular length scales, correlating physical properties with structure is also critical since properties are highly dependent on atomic steps on surfaces, surface defects and local atomic composition. Synergistic fabrication, atomic scale characterization and theoretical modeling are combined to achieve this goal. Nanosystem fabrication and characterization is conducted to contribute to manufacturing and improving understanding of nanoscale systems that have applications in photovoltaics, nanophotonics, and sensors.