Introduction and aim: Micro-CT imaging is becoming an increasingly popular method for evaluating root canal preparation techniques. The purpose of this study was a micro-CT imaging-based comparison of the effects of three different NiTi systems (ProTaper Gold (PTG), ProTaper Next (PTN), and WaveOne (WO)) on root canal morphology after instrumentation. Methods: The study employed a search strategy using four databases (Google Scholar, PubMed, Web of Science, and Cochrane), with identical keyword patterns including micro-CT, rotary, NiTi, instrumentation, and root canal preparation. Results: The results of the study showed that each system had its own advantages and disadvantages. PTG is similar to ProTaper Universal (PTU) but has a gold proprietary processing that provides better cyclic fatigue resistance and greater flexibility. In comparison to PTN, which is designed for rotary users to minimize the number of files and has an advanced swaggering motion that can reduce the risk of instrument fracture, PTG showed comparable volume and surface area enlargement in the coronal third and middle third of the canal. PTN, on the other hand, resulted in less resin removal and better centering ability. WO, a single-file system designed for inexperienced dentists or those seeking simplicity, enabled more centralized biomechanical preparation, particularly in the apical third of the root canal system compared to the shaping ability of PTG. Conclusion: The research emphasizes the significance of data-driven decision-making for selecting the most appropriate NiTi system for specific clinical cases. It highlights the value of micro-CT imaging for objective assessment of root canal preparation techniques and suggests that system choice should consider individual needs and practitioner experience. Ultimately, as endodontics continue to advance, further research and development are vital for more efficient root canal enlargement systems that match the intricacies of the root canal system's original anatomy.