The purpose of this study was to evaluate the root canal preparation in flat-oval root canals of distal roots of mandibular molars treated with either Rotary or Self-Adjusting File (SAF) by using CBCT analysis. Method: Forty human mandibular molars extracted due to non-restorability and periodontal reasons were selected. Teeth were accessed by using high-speed diamond burs. Mesial roots of all teeth were separated at furcation by using a diamond disc.Apical patency of single distal canal was determined. Forty Specimens were randomly divided to two experimental groups (n = 20) according to the instrumentation technique. Group A: Rotary ProTaper, Group B: SAF. Specimens from both groups were scanned using Cone Beam Computed Tomography before and after instrumentation with Rotary ProTaper and SAF. Three levels were chosen for measurements: apex (level 1), middle (level 2) and coronal (level 3). For evaluation of root canal preparation, the differences in pre- and post- instrumentation measurements were obtained for the samples in each group. The values of differences thus obtained were subjected to statistical analysis using independent t-test and the mean values of differences at four coordinates (buccal, lingual, mesial and distal) were obtained at three levels of the canals (apex, middle and coronal). Results: From the statistical analysis, it was observed that both the groups prepared canals satisfactorily. The mean values of differences in pre and post instrumentation measurements were not statistically significant at all three levels. However, at each level the performance of both the instrument systems was different in all four directions. Although the statistical analysis of the coronal, middle and apical third showed no difference between both the groups, the results clearly showed that both the instrument groups differed from each other in preparing flat-oval shaped canals. Conclusion: SAF prepares flat-oval shaped canals homogenously at coronal and middle third, resulting in uniform, and circumferential removal of dentin. However at the apical third, Rotary ProTaper is more effective in canal preparation.