We present a controllable self-assembly method for guiding and positioning nano-scale objects onto a microfabricated template mediated by a genetically engineered polypeptide. Inspired by nature, our group has adapted the different molecular biology based protocols to identify and tailor polypeptides that can recognize and specifically bind to inorganic surfaces. In this paper, we show a three-repeat form of a cell surface selected gold binding polypeptide (GBPI: MHGKTQATSGTIQS). We delineate the procedures including how to identify the polypeptide; how to use this polypeptide for the bottom up self-assembly of semiconducting quantum dots (QDs) onto microfabricated patterns; and finally how to achieve a further level of control over the binding of the polypeptide to microstructures via application of a bias voltage. Our approach opens a new venue for bridging the biological and inorganic domains, and guiding self-assembly of structures and devices from the bottom up.