The structural properties of VO2 thin films, grown on either LSAT or Si substrates by pulsed laser deposition (PLD), are elucidated by means of transmission electron microscopy (TEM) methods. The TEM observations confirmed the successful growth of VO2 by PLD in variable thicknesses, by optimizing the O2 partial pressure and growth temperature. The films adopt a columnar polycrystalline morphology with narrow columns, up to the film thickness height. Four VO2 polymorphs have been detected by electron diffraction and high-resolution TEM (HRTEM) analysis, with M1 being by far the most abundant phase. Post-experimental strain measurements in HRTEM images have revealed that the actual residual strain is minimized due to the columnar morphology of the VO2 grains, as well as intrinsic oxide layers in the VO2/Si epitaxy. The TEM outcomes confirmed the complementary electrical and magnetic measurements in the films, where a transition from a monoclinic M1 to a rutile VO2 R phase has been identified, influenced by the initial percentage of phases in thick VO2 films.