We describe a method to organize nanometer-sized hydrophilic particles into ordered arrays by templating them in the soft, micelle-crystal phases (spherical and cylindrical) of a thermoreversible block copolymer. Small-angle neutron scattering (SANS) with contrast variation is used to show that the dispersed particles (in this case, proteins or silica) form structured arrays by being constrained in the interstitial cavities between the polymer micelles in the ordered micelle crystal. Simple shear is used to macroscopically align both phases of the nanocomposites (micelles and particles) into macro-domains. The temperature-induced order-order transition between templates of spherical and cylindrical micelles is demonstrated as a reversible technique to modify the structure of the templated nanoparticle arrays.