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Microphase-separated block copolymers were introduced as melts into nanoscopic cylindrical pores in alumina membranes via capillary action. The geometric confinement of both lamellar and cylindrical microdomain morphologies of styrene/butadiene block copolymers, PS-b-PBD, was investigated by transmission electron microscopy. Well-developed microphase-separated structures were formed within the resulting nanorods. Polymers that exhibit cylindrical microdomains in the bulk orient with cylindrical microdomains along the nanorod axis due to the preferential segregation of the PBD block to the walls of the pores. The period and packing of the microdomains differ from those observed in the bulk due to an incommensurability between the pore geometry and the natural period and hexagonal packing of the copolymer microdomains. With polymers exhibiting bulk lamellar morphology, confinement forces the formation of concentric cylinders oriented along the nanorod axis. The number of concentric cylinders depends on the ratio of the nanorod diameter to the equilibrium period of the copolymer. Because of the preferential segregation of PBD at the alumina surface, either PBD or PS can form the central core. These results indicate a method by which copolymer microdomains can be manipulated in a simple manner for the fabrication of isolated nanostructures.