Poly(ethylene oxide)-covered CdSe nanorods were prepared and assembled in diblock copolymer templates by floating the block copolymer templates onto aqueous nanorod solutions. The assembly was enabled by consideration of the surface ligand coverage of the nanorods. Alkane-covered CdSe nanorods prepared by state-of-the-art techniques are not compatible with this assembly process. However, poly(ethylene oxide) (PEO)-functionalized CdSe nanorods were successfully used to assemble the nanorods into the channels and pores of diblock copolymer templates. Other water-dispersible CdSe nanorods, such as those covered with 11-mercaptoundecanoic acid (MUA), did not give the desired assemblies. These results are understood by considering the surface energies of the PEO-covered CdSe nanorods in this interfacial assembly process.