Aim To evaluate the effectiveness of a solvent (eucalyptol) in improving filling material removal from canals connected by isthmuses, and the additional cleaning effect of a finishing instrument. Methodology The mesial canals from 32 mandibular molars (Vertucci's type II morphology) were instrumented and filled with the single‐cone technique using Reciproc R25 gutta‐percha points (VDW, Munich, Germany) combined with Sealer 26 (Dentsply, Petrópolis, RJ, Brazil). Each root was then subjected to retreatment using the Mtwo instrument system (VDW), with or without a solvent (n = 16 per group). The volume of filling material in the canals was assessed by micro‐computed tomographic (micro‐CT) scans taken before and after retreatment. Canals with remnants of filling material received a supplementary procedure with the XP‐endo Finisher R instrument (FKG Dentaire, La Chaux‐de‐Fonds, Switzerland), with or without eucalyptol, and another micro‐CT scan was taken. All retreatment procedures were performed inside a cabinet under a controlled temperature (37 °C). Filling material removal was evaluated in the 5‐mm apical canal system for the canal+isthmus space or the isthmus alone. Statistical analyses were performed to compare the removal of filling material with and without eucalyptol, and after a supplementary approach with XP‐endo Finisher R. The level of significance was set at 5% for all statistical tests (P < 0.05). Results The amount of filling material removed from the canal+isthmus with Mtwo instruments was 83.2% when no solvent was used and 83.8% using the solvent (P > 0.05). When the isthmus area was evaluated separately, most specimens were associated with a reduction in the filling material, with no significant difference between the groups with or without using a solvent (P > 0.05). The supplementary step with XP‐endo Finisher R significantly improved removal of filling material from both canal and isthmus area (P < 0.05), regardless of the use of a solvent (P > 0.05). Conclusion The use of eucalyptol did not improve filling material removal from Vertucci's type II molar mesial canals and isthmuses. XP‐endo Finisher R significantly enhanced removal of filling material from the canals and isthmuses.