First lab-on-chip devices based on active transport by biomolecular motors have been demonstrated for basic detection and sorting applications. However, to fully employ the advantages of such hybrid nanotechnology, versatile spatial and temporal control mechanisms are required. Using a thermo-responsive polymer, we demonstrate the selective starting and stopping of modified microtubules gliding on a kinesin-1-coated surface. This approach allows the self-organized separation of multiple microtubule populations and their respective cargoes