Introduction: The aim of this study was to measure the time consumed preparing retrograde cavities in root canals of maxillary molars filled using the GuttaCore (Dentsply Tulsa Dental Specialties, Tulsa, OK) technique and the cold lateral condensation technique (CLC) and to examine the quality of the root-end cavity preparation by ultrasonic tips using micro computed tomographic (micro-CT) scanning. Methods: A total of 24 maxillary molars were included; distobuccal and palatal canals were instrumented to size #40 and size #50, respectively. Teeth were randomly distributed into 2 experimental groups; half of the samples were filled with CLC, and half were filled with the GuttaCore technique. After 2 months, the apical 3 mm of each root apex was resected. A retrograde cavity was then prepared 3 mm deep into the root-end filled canals using ultrasonic tips. The quality of the preparation was first confirmed by a surgical stereomicroscope, and the time required for the root-end preparation was recorded. After root end cavity preparation, all samples were scanned by micro-CT scanning. Results: There was no significant difference between the palatal and distobuccal canals in the time required to prepare a retrograde cavity. Less time was required in the GuttaCore group to remove all root filling material and finish the cavity preparation than in the CLC group (P<.05), especially in the palatal canals. Micro-CT results confirmed that all material was removed from the root-end cavities and the absence of microcracks. Conclusions: GuttaCore was removed in less time from root-end cavities than root filling performed with the CLC technique. No damage to the surrounding dentin was detected by micro-CT scanning in the 2 groups.