A template with macroscopically aligned nanopatterns can be an effective vehicle for arranging nanoscale particles or rods in a particular orientation to achieve their anisotropic properties. A room-temperature process is also desirable for nanoscale patterning of heat-sensitive functional molecules such as organic fluorophores. Here, large-area orientation of nanodomains of block copolymers is demonstrated by simultaneous shearing and solvent vapor annealing at room temperature. The shear-aligned nanodomains are applied to a chemical template for nanoscale patterning of green fluorescent molecules. In addition, the grooved nanochannels obtained from the macroscopically aligned nanodomains work as a physical template for guiding Au nanorods to end-to-end assemblies which exhibit the polarization-dependent plasmonic extinction.