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, ⟨<i>P</i>⟩. Mesopore organization is explored as a function of aging time between sol preparation and filling of the microfluidic channels. Channels filled well be...