Systems and methods for removing material from a packaged electronic device of the type encapsulated with a protective material that forms an outer surface of the device. An exemplary system includes a stage for placing the device in a first position for receiving laser radiation to remove the material by ablation, and for placing the device in a second position for viewing one or more features along the outer surface of the device. An optical system is configured to provide an exterior image, including one or more features along an exposed surface of the device, while the device remains in the second position. A viewing system displays a captured image of the device, including one or more features interior to the protective surface, overlayed with the exterior image for simultaneous viewing of both images so that a position of a first feature present in the captured image can be viewed in relation to a position of a second feature in the exterior image. The combination of the first feature position and the second feature position can be used to define a region of the device for material removal with a laser. In an associated method a captured image of the device is provided, the image including one or more features interior to the protective surface. One or more features along the outer surface of the device are viewed with an optical system while the device remains on a stage, the optical system providing an exterior image. The captured image is combined with the exterior image for simultaneous viewing so that the position of a first feature present in the captured image can be viewed in relation to the position of a second feature in the exterior image. A region is defined for decapsulation based on the position of the first feature relative to the position of the second feature.