The aim of this study was to evaluate the effects that various commonly used instruments have on root surface morphology, the obturating material, and the interface between the obturation and the root canal walls following root-end resection in vitro. Sixty human single-rooted teeth with fully formed apices were collected and decoronated. The root canals were instrumented, and then obturated with thermoplasticized gutta-percha using AH-26 as the sealer. The roots were randomly divided into 12 different groups, and apical root-end resections were performed using eight different instrument configurations, and two different directions in which the bur moved across the root face in relation to its direction of rotation. Epoxy resin replicas of the resected root ends were examined using scanning electron microscopy. Each instrument produced a characteristic surface finish on the resected root end that mirrored its cutting profile. Irrespective of the design of the bur used, smearing and shredding of the gutta-percha across the root face occurred only when the handpiece was moved across the root face in reverse direction in relation to the direction of rotation of the bur. To ensure minimal disruption and distortion of the root filling and to prevent shredding of the gutta-percha interface, care should be taken to ensure that the final pass of the bur across the root canal is in the correct direction in relation to its direction of rotation.