Rayleigh instabilities in thin polymer films confined within nanoporous alumina membranes were studied. Thin films of poly(methyl methacrylate) (PMMA) were prepared by filling cylindrical nanopores in an anodic aluminum oxide (AAO) membrane with a PMMA solution in chloroform followed by solvent evaporation. When the PMMA nanotubes were annealed above the glass transition temperature (Tg), undulations in the film thickness were observed that were induced by a Rayleigh instability. The amplitude of the undulations increased with time and eventually bridged across the cylindrical nanopore in the AAO membrane, resulting in the formation of polymer nanorods with periodic encapsulated holes. A similar behavior was observed when PMMA films were confined within carbon nanotubes (CNTs). The Rayleigh instabilities in these confined geometries offer a novel means of controlling and fabricating the polymer nanostructures. These compartmentalized nanorods may have potential applications as delivery devices.