The objective of this study was to evaluate the efficacy of reciprocating instruments in the removal of bioceramic and epoxy resin-based sealers using micro-CT analysis. Root canals of 40 extracted human teeth were instrumented with a size R25 Reciproc instrument. Specimens were randomly divided into two groups (n = 20) according to the root canal filling material. In the first group, root canals were obturated with AH Plus sealer and Reciproc R25 gutta-percha. In the second group, a combination of bioceramic gutta-percha (TotalFill BC) and bioceramic sealer (TotalFill BC) was used. After one week, the retreatment of all specimens was performed using Reciproc instruments. To analyze the differences in the filling remnants, specimens were scanned in a micro-CT device after obturation and after the retreatment procedure. Statistical analysis was performed using the Mann-Whitney U test (p < 0.05). A combination of bioceramic sealer and bioceramic gutta-percha was more effectively removed from canals using a reciprocating instrument, with a filling remnants volume of 4.01 ± 3.13 mm3, in comparison to the combination of epoxy resin-based sealer and gutta-percha (6.96 ± 2.70 mm3) (p < 0.05). A reciprocating instrument was more effective in removing bioceramic sealers than epoxy resin-based sealers, although none of the root canal filling materials were completely removed from the root canals.