Introduction: The introduction of the Nickel Titanium (NiTi) alloy for the manufacture of endodontic instruments has been revolutionary. NiTi alloy due to their increased flexibility and shape memory, potentially allow shaping of narrow, curved root canals without causing aberrations. Material and Methods: The present study aimed to compare canal preparation between 4 different NiTi rotary file systems (protaper next–group 1; M–two –group 2; Revo–S–group 3; V–taper files;group 4;  Hand Kfiles–group 5) and one stainless steel using Computed Tomography, based on following factors: Canal transportation and Centering Ability. In all the groups, before preparation canal localization was done through CBCT measurements. Mesial and Distal distances from canal center were measured at 3 mm, 6 mm and 9 mm from coronal end. Results: When comparing the overall canal shift, at 9 mm location, mean mesial shift ranged from 0.64±0.53 mm to 1.29±0.68 mm and statistically, there was a significant difference among groups. Post hoc test revealed that except for a significant difference between Group I and V at 9 mm location on the mesial side, none of the between group differences were significant. There was no significant difference in the overall transportation of canal in different study groups at different locations. Conclusion: The canal transportation observed at different reference points varied significantly. At 3mm, Mtwo file system showed least canal transportation whereas at 6mm, V–Taper showed least canal transportation and at 9mm RevoS showed least canal transportation. The maximum canal transportation was observed at 3mm, 6mm and 9mm by Hand K–files. This trend clearly proved that skills of the operator and design of the cutting edge of the instrument played a pivotal role in canal transportation and centering ability.