Background/Objectives: The damage assessment of dental instruments, such as endodontic files, is crucial to ensure patient safety and treatment quality. Conventional scanning electron microscopy (SEM) has been the gold standard for this purpose; however, its limited accessibility and complex sample preparation protocols hinder its routine use in clinical settings. This study proposes a novel system that leverages digital photography and advanced image processing techniques as a viable alternative to SEM. Methods: Our system accurately detects early instrument damage by capitalizing on the high resolution of digital images. Its exceptionally user-friendly interface, portability, and key features make it highly suitable for daily clinical practice. Results: Our findings suggest that the proposed system provides image quality comparable to SEM. Conclusions: Image stacking provides a practical, efficient, and objective method for assessing endodontic instruments’ morphology. By detecting early damage, this system significantly improves the safety and quality of endodontic procedures, especially for reusable NiTi files, instilling confidence and security in its use. It offers a cost-effective and user-friendly alternative to traditional methods such as visual inspection and SEM, making it a comfortable and confident choice for both research and clinical settings.