We have developed a new method for processing distorted high-resolution scanning transmission electron microscopy (STEM) images. The method is based on finding the displaced vertices in the experimental STEM image and warping to geometrically correct reference grid of the object. As a reference grid for warping a structural model obtained using a high-resolution transmission electron microscopy (HRTEM) analysis of the area of interest is utilised. Combined with quantitative HRTEM analysis the IMAGE-WARP method provides a real-space restoration of high-resolution high-angle annular dark-field (HAADF) STEM images without affecting the original Z-contrast information. The method can be applied to extract valuable compositional atomic-column data from any HAADF-STEM image of any kind of bulk crystals with local occupancy or chemistry fluctuations, stacking faults, special grain boundaries or interfaces, for which we have an available structural model. After the warping, distortion-corrected images can be further enhanced using conventional image-filtering techniques, and finally quantified with HAADF-STEM image simulations. The applicability of the IMAGE-WARP method was illustrated using experimental HAADF-STEM images of a strontium titanate crystal disrupted with a Ruddlesden-Popper-type antiphase boundary.