Tungsten trioxide is a binary oxide that has potential applications in electrochromic windows, gas sensors, photo-catalysts, and superconductivity. Here, we analyze the crystal structure of atomically flat epitaxial layers on YAlO3 single crystal substrates and perform nanoscale investigations of the ferroelastic twins revealing a hierarchical structure at multiple length scales. We have found that the finest stripe ferroelastic twin walls along pseudocubic <100>axes are associated with cooperative mosaic rotations of the monoclinic films and the larger stripe domains along pseudocubic <110> axes are created to reduce the misfit strain through a commensurate matching of an effective in-plane lattice parameter between film and substrate. The typical widths of the two fine and larger stripe domains increase with film thickness following a power law with scaling exponents of ∼0.6 and ∼0.4, respectively. We have also found that the twin structure can be readily influenced by illumination with an electron beam or a tip-based mechanical compression.