This study aimed to use micro-computed tomography (micro-CT) imaging to evaluate the efficacy of the reciprocating and rotary systems for the removal of root filling materials in comparison with hand files. Thirty maxillary incisor teeth were prepared with ProTaper Universal (PTU) system, filled using cold lateral condensation and randomly divided into three groups of ten teeth each. The root fillings were removed with WaveOne Reciprocating and ProTaper Universal Re-treatment (PTU-R) systems and hand files. Micro-CT was used to scan the specimens before and after each treatment step. Percentage of volume of residual root filling was measured. The operating time was recorded. PTU-R instruments yielded better results for removing filling material, even though there was no statistically significant difference between PTU-R and WaveOne groups. Reciprocating and rotary systems showed similar performances in terms of efficacy and operating time for root filling removal.