OBJECTIVES: The aim of this study was to compare the efficacy of rotary and reciprocating techniques for removing filling material from root canals, using micro-computed tomography (micro-CT) imaging. MATERIALS AND METHODS: The distal root canals of 42 human mandibular molars were instrumented with hand files up to size 40 according to a step-down technique and obturated with gutta-percha and an epoxy resin-based sealer using Tagger's hybrid technique. Teeth were divided into six groups (n = 7) according to the instruments used for removal of filling material: group PTUR (Protaper Universal Retreatment), group W40 (WaveOne 40.08), group R40 (Reciproc 40.06), group R50 (Reciproc 50.05), group W25/W40 (WaveOne 25.08/40.08), and group R25/R40/R50 (Reciproc 25.08/40.06/50.05). Teeth were scanned with a micro-CT device before and after use of the instruments to calculate the percentage of remaining filling material. Data were compared using one-way ANOVA and Fisher's LSD test at 5 % significance level. RESULTS: The mean percentage of remaining filling material was significantly lower when canals were retreated with the set of instruments R25/R40/R50 and single instruments W40 and R50 compared with the set of instruments W25/W40 (P < 0.05), which promoted material compaction in the apical region. CONCLUSION: None of the retreatment techniques removed the root fillings completely. PTUR instruments performed equally effective regarding filling removal compared with W40, R40, R50, W25/W40, and R25/R40/R50. For WaveOne, the use of a single instrument (size 40, taper 0.08) was more effective in removing filling material, while for Reciproc showed similar cleaning ability using single instrument or combination of instruments. CLINICAL RELEVANCE: The results of this in vitro study provide consistent information on filling material removal capacity of mechanized systems during retreatment at the different root canal thirds.