Investigating the molecular gas in the inner regions of protoplanetary disks (PPDs) provides insight into how the molecular disk environment changes during the transition from primordial to debris disk systems. We conduct a small survey of molecular hydrogen (H[Subscript: 2]) fluorescent emission, using 14 well-studied Classical T Tauri stars at two distinct dust disk evolutionary stages, to explore how the structure of the inner molecular disk changes as the optically thick warm dust dissipates. We simulate the observed Hi-Lyman α-pumped H[Subscript: 2] disk fluorescence by creating a 2D radiative transfer model that describes the radial distributions of H[Subscript: 2] emission in the disk atmosphere and compare these to observations from the Hubble Space Telescope. We find the radial distributions that best describe the observed H[Subscript: 2] FUV emission arising in primordial disk targets (full dust disk) are demonstrably different than those of transition disks (little-to-no warm dust observed). For each best-fit model, we estimate inner and outer disk emission boundaries (r[Subscript: in] and r[Subscript: out]), describing where the bulk of the observed H[Subscript: 2] emission arises in each disk, and we examine correlations between these and several observational disk evolution indicators, such as n[Subscript: 13–31], r[Subscript: in, CO], and the mass accretion rate. We find strong, positive correlations between the H[Subscript: 2] radial distributions and the slope of the dust spectral energy distribution, implying the behavior of the molecular disk atmosphere changes as the inner dust clears in evolving PPDs. Overall, we find that H[Subscript: 2] inner radii are ~4 times larger in transition systems, while the bulk of the H[Subscript: 2] emission originates inside the dust gap radius for all transitional sources.