Ultramicrotomy, the technique of cutting nanometers-thin slices of material using a diamond knife, was applied to prepare transmission electron microscope (TEM) specimens of nanoporous poly(methylsilsesquioxane) (PMSSQ) thin films. This technique was compared to focused ion beam (FIB) cross-section preparation to address possible artifacts resulting from deformation of nanoporous microstructure during the sample preparation. It was found that ultramicrotomy is a successful TEM specimen preparation method for nanoporous PMSSQ thin films when combined with low-energy ion milling as a final step. A thick, sacrificial carbon coating was identified as a method of reducing defects from the FIB process which included film shrinkage and pore deformation.