This study compared the percentage reduction of total obturation materials, gutta-percha and sealer, using two rotary file systems with/without solvent in retreating C-shaped root canals and to evaluate the effect of the solvent on instrument separation. C-shaped root canals were scanned using micro-CT to identify the root canal morphology and randomly assigned to four groups (n = 12). Retreatment was performed using ProTaper Universal Retreatment (PTUR) or XP-endo systems with/without solvent. The number of separated instruments were recorded. The samples were scanned pre- and post-retreatment. The percentage reduction of total obturation materials, gutta-percha and sealer, were calculated. The percentage reduction of gutta-percha in the PTUR without solvent group was significantly lower than the other groups (P = 0.018). The number of separated instruments in the solvent groups were significantly lower than the no solvent groups (P < 0.05). Solvent increased gutta-percha removal, when using PTUR and decreased the occurrence of separated instruments for both systems.