Anodic aluminum oxide (AAO) membranes were used as templates to control orientation of an ion-channel forming columnar mesophase obtained by self assembly of a wedge-shaped sulfonate molecule. Inside the AAO structure, the director vector of the mesophase is oriented parallel to the pore axis due to the confinement effect. The molecular arrangement induced by the spatial confinement within the pores is extended over several microns into the remnant film on the AAO surface. The homeotropic alignment of the channels promotes unidimensional ion conduction through the film plane, which is manifested by a considerable increase in conductivity relative to isotropic samples.