Single molecule tracking (SMT) methods are employed to characterize the in-plane alignment and order of cylindrical mesopores in flow-aligned surfactant-templated silica monoliths prepared within glass microfluidic channels. The majority of dye molecules observed in wide-field fluorescence videos of these samples exhibit one-dimensional (1D) diffusive motions. Orthogonal regression analysis of these motions provides a measure of the mesopore orientation distribution function, which in turn is used to quantify the mesopore order via a two-dimensional orientational order parameter, < P >. Mesopore organization is explored as a function of aging time between sol preparation and filling of the microfluidic channels. Channels filled well before gelation of the sol are shown to incorporate large monodomains having average pore alignment within a few degrees of the flow direction. These monodomains extend over several millimeters and yield aging-time-independent < P > values larger than similar to 80. In contrast, channels filled near the time of sol gelation yield monoliths with misaligned pores that are also more disordered, having < P > approximate to 0.35. The SMT results are compared to those from small-angle X-ray scattering anisotropy experiments; these data are consistent across the range of samples investigated. A model describing the aging-time dependence of sol organization is presented. These studies demonstrate that well-aligned mesoporous silica monoliths can be obtained by simple flow alignment procedures but that short sol aging times are required in order to achieve optimum pore organization.