Removal of resin-based root canal filling materials may cause serious problems during root canal retreatment. This study compared the working time and amount of canal enlargement when different resin-based root canal filling materials were removed with K3 rotary instruments with or without heat-softening using System B. Root canal sealer/filling point combinations tested were Epiphany/Resilon, SuperBond/Resilon, SuperBond/gutta-percha, and Canals N/gutta-percha. The materials were filled into simulated curved resin canals and removed with K3 instruments in a standardized crown-down procedure. In terms of working time, Epiphany/Resilon required a significantly longer working time than the others. However, heat application with System B significantly reduced the working time for the removal of Epiphany/Resilon. In terms of canal enlargement, there were no significant differences among the tested groups as determined with digital morphometry. It was thus concluded that Epiphany removal with K3 rotary instruments might result in extended working time, but which could be reduced with heat-softening using System B.