Background: The effectiveness of endodontic retreatment essentially depends on the cleaning and/or disinfection processes. In this context, the removal of root canal filling materials plays a crucial role. Aims: To assess the efficacy of passive ultrasonic irrigation (PUI), EndoActivator system (EAS), and XP-endo Finisher R (XPEFR) as additional cleaning techniques to remove the remaining root canal filling materials from flattened root canals. Subjects and Methods: Thirty-six similar flattened distal root canals of extracted human first lower molars were selected by micro-computed tomography (micro-CT) and then instrumented and filled. After the initial retreatment procedures, the residual volume of root canal filling materials was assessed by micro-CT (V1). Then, the specimens were divided into three groups (n. 12), according to the additional cleaning technique and submitted to another micro-CT scan (V2). Statistical Analysis Used: Analysis of variance and Games-Howell tests ( P < 0.05). Results: The percentage reduction in the residual volume of root canal filling materials reached by PUI, EAS, and XPEFR was 28.38%, 28.12%, and 43.52%, respectively, considering the total space of the root canal ( P > 0.05). In the apical third, these values were 20.05%, 21.54%, and 48.82% ( P < 0.05). Conclusions: Additional cleaning techniques enabled removing a greater amount of root canal filling material from flattened distal root canals of extracted human first lower molars. Considering the total space of the root canal, there were no statistically relevant differences among the groups. In the apical third, XPEFR performed better.