Modern electro-optical systems often include several channels for imaging at different bands. These systems are capped with a window assembly in which the optical windows are cemented to a frame using dedicated adhesives intended to seal the system’s internal optics from the outside environment. Such window assemblies may include several optical windows made of different materials, depending on the necessary spectral bands, and are usually very expensive. Occasionally, these windows, become damaged due to exposure to severe environments, and require replacement. In such a case, there is a need for a detachment process to remove and replace only the defective part without damaging the rest of the windows or the metal frame. In this work, we have developed a dedicated tool which enables cost-effective and selective detachment of only the defective parts without any damage to the rest of the window assembly. The detachment process is based on a 3-axis hotwire automated system that was inspired by the foam cutting industry. An electrical current is passed through a hotwire which is then used to selectively decompose the adhesive along the bond line. Parameters such as wire voltage, wire tension, and velocity were selected to yield the best performance, namely, quick and safe removal of the part. The flexibility of the system’s design allows for detaching windows of different geometries, materials, and sizes.