Understanding the structure of interstellar clouds is integral to painting a large-scale picture of star formation in the Milky Way. Historically, analyzing the structure of clouds from two-dimensional “plane-of-the-sky” maps to build a physical picture has been challenging. Thanks to new “3D dust maps” (Leike et al. 2020), recent work (Zucker et al. 2021) has suggested that clouds have two prominent components: a thin, dense, inner layer and a broad, sparse, outer layer. However, we do not know how the 3D dust structure maps on to the physical conditions of the gas. We leverage recent numerical simulations (Smith et al. 2020) of highly resolved interstellar clouds in a Milky Way-like Galaxy to test how the thermal and chemical structure of clouds is affected by the physical conditions occurring in the simulated galaxy. Extracting molecular clouds from feedback-dominated numerical simulations, we measured the clouds’ radial density profiles in multiple tracers, such as molecular and atomic hydrogen, carbon monoxide, and total volume density of hydrogen. While observed clouds have atomic envelopes that extend ~10-15 pc, we find that simulated cloud atomic envelopes extend only ~2-3 pc. Further analysis reveals that the radial profiles of simulated clouds are highly non-symmetric and were heavily influenced by supernova feedback, creating a shock structure that drastically reduced the extent of their atomic envelopes. The developed pipeline from the preceding analysis can be used on future ISM simulations to compare simulated cloud structure to observed cloud structure.