Mesoporous thin films are prepared using a simple sol-gel technique. Using lithographically patterned (100)-oriented substrates and a dip-coating method reproducible alignment of the pores across the substrate surface can be obtained. The pores preferentially align parallel to the long side of the channels etched into the surface. The channels within the aligned films are subsequently filled with cobalt (to form nanowire-type structures) using a supercritical fluid inclusion technique, to allow high-resolution imaging of the pore by using secondary electron microscopy. The channel structure imposes a strain on the mesoporous arrangement resulting in some variation in d-spacings compared to simple films. The results indicate that the topographic structure can be used to engineer the placement and directionality of the pore structure and the potential of the aligned mesostructures are discussed.