Objective The aim of this article was to evaluate the influence of mesial root canal preparation of mandibular molars with the reciprocal systems (RCP) and self-adjusting file (SAF) in the incidence of voids spaces in endodontic obturation performed by modified continuous wave compaction (MCWC) technique, through images obtained in micro-computed tomography (micro-CT). Materials and Methods Mesial roots of 15 mandibular molars, with two independent root canals, were divided into three groups (n = 5/roots), according to the endodontic instrumentation strategy (RCP, SAF, and twisted file [TWF]). After the root canals (n = 10, for each instrumentation system) were filled with MCWC, images of each specimen were obtained by micro-CT followed by three-dimensional reconstruction. The percentage of voids was obtained (in mm³) in relation of the total volume, cervical–middle, and apical thirds. Statistical Analysis The data obtained were submitted to statistical analysis by Kruskal–Wallis and Dunn tests (p < 0.05). Results With respect to the total volume of root canal, TWF demonstrated a lower percentage in comparison to SAF (p < 0.05). No significant difference was obtained between TWF and RCP or RCP and SAF (p > 0.05). In the apical third, RCP showed a smaller percentage of voids when compared with SAF (p < 0.05); however, TWF demonstrated similarity with RCP and SAF (p > 0.05). The middle–cervical third exhibited no statistically difference between TWF and RCP or RCP and SAF (p > 0.05), whereas TWF was lower than SAF (p < 0.05). Conclusion Root canal preparation of mesial root of mandibular molars with TWF provides a lower incidence of voids in the endodontic filling performed by MCWC. Article published online: 30 January 2024 © 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/) Thieme Medical and Scientific Publishers Pvt. Ltd. A-12, 2nd Floor, Sector 2, Noida-201301 UP, India