Nature has evolved dynamic, non-equilibrium mechanisms for assembling hierarchical complexes of nanomaterials. A critical element to many of these assembly mechanisms involves the active and directed transport of materials by biomolecular motor proteins such as kinesin. In the present work, nanocrystal quantum dots (nQDs) were assembled and organized using microtubule (MT) filaments as nanoscale scaffolds. nQD density and localization were systematically evaluated by varying the concentration and distribution of functional groups within the MT structure. Confining nQD attachment to a central region within the MT enabled unaffected interaction with kinesin necessary to support active transport of nQD−MT composites. This active transport system will be further refined to control the optical properties of a surface by regulating the collective organization of nQD−MT composites.