Aim: The aim of the study was to compare the changes in angle of curvature, transportation and centering ratio after instrumentation in M3 Pro Gold system and M Pro system Pro Taper Universal system was used as gold standard and reference for comparison. Materials and Methods: Thirty human mandibular first molars were selected. Teeth were randomly allocated into three groups (n= 10): Group 1: M3 Pro Gold; Group 2: M Pro; Group 3: Pro Taper Universal. Cone Beam Computed Tomography (CBCT) were taken before and after preparation measurements were made using On Demand software. Evaluation of angle of curvature was done using Schneider's method.  Transportation and centering ratio were evaluated using Gambill's method. Comparison between 3 groups was performed by using One Way ANOVA test followed by Tukey`s Post hoc test for multiple comparisons. Results: After root canal preparation significant difference in the change of canal curvature values were found, Pro Taper Universal showed the least change and M Pro showed the highest change (p = 0.0001), while canal transportation results showed significant difference between all groups at all levels as M3 Pro Gold showed the least transportation and M Pro showed the highest transportation (P = 0.0001). Centering ratio results showed significant difference between all groups at all levels as M3 Pro Gold was better centralized in root canal in comparison to M Pro and Pro Taper Universal (p = 0.0001). Conclusion: M3 Pro Gold better respected the original canal anatomy and better conserved root dentine structure as compared to M Pro and Pro Taper Universal.