Objectives: The aim of this study was to assess the potential of a smear-layer removing agent (citric acid) vs. an accepted gutta-percha-softening agent (Xylol) as an alternative substance for removing the root canal filling materials, while investigating the potential for associated demineralization effects. Materials and Methods: Seventy healthy, recently extracted premolars were used, ten as control, with sixty with their canals enlarged, shaped and cleaned and obturated using lateral compaction. Teeth were distributed into 3 groups as follows: 1) no solvent and mechanical removal of the filling materials; 2) 1ml of Xylol for 1 minute followed by mechanical removal; and 3) 10% citric acid for 1 minute followed by mechanical removal. Two sections of the root were used, one for Raman spectroscopy analysis to evaluate morphological changes in dentine surface and the other for micro-hardness testing (Vickers). Results: The use of 10% citric acid in in the removal of gutta-percha and sealer was more effective than the Xylol and mechanical group (p<0.05), presented less remnants of filling material debris and with non-observable demineralizing effects. Conclusion: Citric acid might be considered as a viable alternative in the removal of gutta-percha and sealer during root canal retreatment.Clinical Relevance: This research showed how citric acid can be used as an alternative in endodontic retreatment; how efficiently removed the filling material without damaging the dental tissue.