An array of aligned carbon nanotubes (CNTs) was incorporated across a polymer film to form a well-ordered nanoporous membrane structure. This membrane structure was confirmed by electron microscopy, anisotropic electrical conductivity, gas flow, and ionic transport studies. The measured nitrogen permeance was consistent with the flux calculated by Knudsen diffusion through nanometer-scale tubes of the observed microstructure. Data on Ru(NH3)6(3+) transport across the membrane in aqueous solution also indicated transport through aligned CNT cores of the observed microstructure. The lengths of the nanotubes within the polymer film were reduced by selective electrochemical oxidation, allowing for tunable pore lengths. Oxidative trimming processes resulted in carboxylate end groups that were readily functionalized at the entrance to each CNT inner core. Membranes with CNT tips that were functionalized with biotin showed a reduction in Ru(NH3)6(3+) flux by a factor of 15 when bound with streptavidin, thereby demonstrating the ability to gate molecular transport through CNT cores for potential applications in chemical separations and sensing.