We aimed to analyze the morpho-geometric changes of the root canal system created by two rotary systems (TF Adaptive and BioRace) using micro-CT technology. Two concepts of rotary file system kinematics, continuous rotation and adaptive kinematics, were used in root canal preparation. Twenty mandibular molars (n = 20) were selected with the following criteria: the teeth have mesial roots with a single and continuous isthmus connecting the mesiobuccal and mesiolingual canals (Vertucci’s Type I configuration) and distal roots with independent canals. Teeth were scanned at a resolution of 14 μm. Canals were divided equally into two groups and then enlarged sequentially using the BioRace system and TF Adaptive system according to manufacturer protocol. Co-registered images, before and after preparation, were evaluated for morphometric measurements of canal surface area, volume, structure model index, thickness, straightening, and un-instrumented surface area. Before and after preparation, data were statistically analyzed using a paired sample t-test. After preparation, data were analyzed using an unpaired sample test. The preparation by both systems significantly changed canal surface area, volume, structure model index, and thickness in both systems. There were no significant differences between instrument types with respect to these parameters (p > 0.05). TF Adaptive was associated with less straightening (8% compared with 17% for BioRace in the mesial canal, p > 0.05). Both instrumentation systems produced canal preparations with adequate geometrical changes. BioRace straightened the mesial canals more than TF Adaptive.