Herein we report on the alignment of mesoporous silica, a potential host for sub-10 nm nanostructures, by controlling its deposition within patterned substrates. In-depth characterization of the correlation lengths (length of a linear porous channel), defects of the porous network (delamination), and how the silica mesopores register to the micro meter-sized substrate pattern was achieved by means of novel focused ion beam (FIB) sectioning and in situ SEM imaging, which to our knowledge has not previously been reported for such a system. Our findings establish that, under confinement, directed deposition of the Sol within channeled substrates, where the cross-sectional aspect ratio of the channels approaches unity, induces alignment of the mesopores along the length of the channels. The pore correlation length was found to extend beyond the micrometer scale, with high pore uniformity from channel to channel observed with infrequent delamination defects. Such information on pore correlation lengths and defect densities is critical for subsequent nanowire growth within the mesoporous channels, contact layout (electrode deposition etc.), and possible device architectures.