The aim of this study was to examine the additional effect of activated irrigation protocols (sonic activated irrigation and laser activated irrigation) in combination with sodium hypochlorite and thymol-based solvent activation on the removal of the filling remnants left after the root canal retreatment. In this study, 37 human extracted molars were used. The root canals were instrumented by rotary ProTaper Next system and filled with epoxy resin-based sealer and the combination of continuous-wave and hot injection technique. The canals were retreated by WaveOne Gold primary red file and rinsed according to the standard final irrigation protocol (sodium hypochlorite and ethylenediaminotetraacetic acid). Subsequently, specimens were randomly divided into four groups according to the additional irrigation step. In Group 1, the additional irrigation was performed with the EndoActivator in combination with NaOCl. In Group 2, the thymol-based solvent was laser activated. In Group 3, the additional irrigation was performed with laser activation (LAI) of NaOCl. In Group 4, the thymol-based solvent was used with EndoActivator. Micro-CT scan was performed after the filling, after the retreatment, after the standard irrigation protocol, after the additional step to the irrigation protocol in order to measure the volume of the remaining filling material. Significantly reduced amount of filling material after chemomechanical preparation (p = 0.015) was found in all groups. However, in either sample the filling material was not completely removed. If we look at the reduction of the filling material volume after the additional rinsing of the canals by groups (in relation to the final canal irrigation), no significant reduction was found in any group (p> 0.05). No significant removal of the filling material by additional irrigation (p> 0.05) was demonstrated, as did the difference between the various activation techniques. Additional activation rinsing of the canals did not contribute to the reduction of filler volume within the canals.