Abstract Hyperbolic phonon polaritons (HPhPs) are hybrid excitations of light and coherent lattice vibrations that exist in strongly optically anisotropic media, including two-dimensional materials (e.g., MoO3). These polaritons propagate through the material’s volume with long lifetimes, enabling novel mid-infrared nanophotonic applications by compressing light to sub-diffractional dimensions. Here, the dispersion relations and HPhP lifetimes (up to ≈12 ps) in single-crystalline α-MoO3 are determined by Fourier analysis of real-space, nanoscale-resolution polariton images obtained with the photothermal induced resonance (PTIR) technique. Measurements of MoO3 crystals deposited on periodic gratings show longer HPhPs propagation lengths and lifetimes (≈2×), and lower optical compressions, in suspended regions compared with regions in direct contact with the substrate. Additionally, PTIR data reveal MoO3 subsurface defects, which have a negligible effect on HPhP propagation, as well as polymeric contaminants localized under parts of the MoO3 crystals, which are derived from sample preparation. This work highlights the ability to engineer substrate-defined nanophotonic structures from layered anisotropic materials.