The mesostructure loss kinetics are measured as a function of the orientation of micelles in 2D hexagonal close packed (HCP) columnar mesostructured titania thin films using in situ grazing incidence small angle X-ray scattering (GISAXS). Complementary supporting information is provided by ex situ scanning electron microscopy. Pluronic surfactant P123 acts as the template to synthesize HCP structured titania thin films. When the glass substrates are modified with crosslinked P123, the micelles of the HCP mesophase align orthogonal to the films, whereas a mix of parallel and orthogonal alignment is found on unmodified glass. The rate of mesostructure loss of orthogonally oriented (o-HCP) thin films (∼60 nm thickness) prepared on modified substrate is consistently found to be less by a factor of 2.5 ± 0.35 than that measured for mixed orientation HCP films on unmodified substrates. The activation energy for mesostructure loss is only slightly greater for films on modified glass (155 ± 25 kJ mol(-1)) than on unmodified (128 kJ mol(-1)), which implies that the rate difference stems from a greater activation entropy for mesostructure loss in o-HCP titania films. Nearly perfect orthogonal orientation of micelles on modified surfaces contributes to the lower rate of mesostructure loss by supporting the anisotropic stresses that develop within the films during annealing due to continuous curing, sintering and crystallization into the anatase phase during high temperature calcination (>450 °C). Because the film thickness dictates the propagation of orientation throughout the films and the degree of confinement, thicker (∼250 nm) films cast onto P123-modified substrates have a much lower activation energy for mesostructure loss (89 ± 27 kJ mol(-1)) due to the mix of orientations found in the films. Thus, this kinetic study shows that thin P123-templated o-HCP titania films are not only better able to achieve good orthogonal alignment of the mesophase relative to thicker films or films on unmodified substrates, but that alignment of the mesophase in the films stabilizes the mesophase against thermally-induced mesostructure loss.