The ability to create small-scale material patterns using lithography has been limited by the feature sizes and assembly of the master stamping system. Developing a simple and robust robotically automated patterning technique for both organic and inorganic materials, which is able to be actively controlled down to scales smaller than the operating features, would enable new capabilities and directions in research. Here, a novel method is presented to form patterns of defined shape and distribution via automated assembly along with force-controlled microstamping. Robotic assembly based particle templates and pyramid structures were used to create controlled distributions of materials. Systems including quantum dots and biomolecules were patterned, demonstrating our ability to create repeatable geometries with size scales smaller than the master stamping system. These patterns were also utilized for constraining cell adhesion and spreading. This work has potential applications in diverse areas from building molecular circuits to probing biological pattern formation.