The study aimed to evaluate the efficiency of the BTR-Pen system in removing different types of instrument fragments from root canals and to assess its effect on fracture resistance of the roots after the removal of the instruments. One hundred thirty human teeth were divided into 10 groups (2 control groups and 8 study groups) according to the localization and type of the fractured fragment as well as the retrieval techniques. Broken instruments were extracted either with BTR-Pen system loops or removed using solely ultrasonic tips. The success rate of instrument removal and consumed time were recorded. All the teeth were subjected to a load at a 1 mm/min rate in a universal testing machine for mechanical testing. The success of removing broken instruments using the BTR-Pen and ultrasonic was 86.7% and 83.3%, respectively (p > 0.05). When the time is compared, the BTR-Pen system (23.97 ± 8.35 min) showed similar results to that of the ultrasonic technique (24.1 ± 8.28 min) (p > 0.05). The BTR-Pen group required less force to fracture than the ultrasonic group (p = 0.024). In conclusion, the BTR-Pen and ultrasonic groups showed no significant difference in terms of the success rate and removal time. The roots that underwent instrument removal using the BTR-Pen system had less fracture resistance.