Embodiments of the disclosure provide apparatus and methods for localized stress modulation for overlay and edge placement error (EPE) using electron or ion implantation. In one embodiment, a process for correcting overlay error on a substrate generally includes performing a measurement process in a metrology tool on a substrate to obtain a substrate distortion or an overlay error map, determining doping parameters to correct overlay error or substrate distortion based on the overlay error map, and providing a doping recipe to a doping apparatus based on the doping parameters determined to correct substrate distortion or overlay error. Embodiments may also provide performing a doping treatment process on the substrate using the determined doping repair recipe, for example, by comparing the overlay error map or substrate distortion with a database library stored in a computing system.