Accurate structure analysis of epitaxial perovskite thin films is a fundamental step towards the ability to tune their physical properties as desired. Precession-assisted electron diffraction tomography (PEDT) has proven to be an effective technique for performing ab initio structure solutions and refinements for this class of materials. As the film thickness or the region of interest (ROI) decrease in size, the capacity to collect PEDT data with smaller electron beams is a key parameter and ROI tracking becomes a major issue. To circumvent this problem, we considered here an alternative approach to acquiring data by combining PEDT with a scan over an area, extracting the intensities collected at different positions and using them to perform accurate structure refinements. As a proof of concept, a Scanning Precession Electron Tomography (SPET) experiment is performed on a 35 nm thick perovskite PrVO$_3$ (PVO) film deposited on a SrTiO$_3$ (STO) substrate. This way, it was possible to detect small changes in the PVO structure along the film thickness, from the variation in unit cell parameters to atomic positions. We believe that SPET has the potential to become the standard procedure for the accurate structure analysis of ROIs as small as 10 nm.