Introduction: Mechanical instrumentation is quite effective at reducing the numbers of bacteria in the canal. There are three main areas in which engine driven instrumentation has been modified over the years as more and more file systems are introduced to the market. Aim of the study: The aim of this study is to compare Protaper Next, Plex v and Endostar E3 as regarding the root canal preservation in the form of canal transportation in mesial roots of mandibular molars. Material and Methods: A total of 45 mandibular molars were selected and randomly divided into three experimental groups (n=15) according to the instrumentation technique: ProTaper next, Endostar E3 and Plex V rotary file systems. Specimens from each groups were scanned using CBCT before and after instrumentation to evaluate the canal preparation, number of prepared and unprepared surfaces at three thirds of root canal in each instrument system. Data were statistically analyzed, and the significance level was set at p<0.05. Results: The results showed no statistically significant difference between the groups with P-values of 0.562, 0.83 and 0.732 for Curvature, Radius and apex-CEJ distance respectively. Conclusion: All systems; can effectively shape curved root canals with minimal transportation, produce well centered preparations, with sufficient enlargement of root canals and without excessive removal of dentin. Plex V rotary file system is preferred over other systems in cases with insufficient dentin thickness at the coronal level.