The aim of this finite element stress analysis (FEA) study was to assess the effect of separated files (SF) that were broken at two levels (at apical 4 and 9 mm) on the biomechanics of premolars and to determine if removal techniques affect stresses. Six lower premolar teeth were screened on computerized microtomography (micro-CT), standard access cavities were prepared, working lengths were determined, and root canals were prepared (Protaper files, Protaper Universal, Dentsply, Switzerland). Notches were created on the final shaping-file F3 at points 4 and 9 mm from the file tips, inserted in the canals, and squeezed at the apical to break. The roots were rescreened, and SFs were removed by using a Masseran kit (MK; Micro Mega, France), ultrasonic tips (UT; Satelec, Acteon group, France), and the bypass (BP) technique. Final scans were obtained and converted into three-dimensional FEA models. The following conditions were then simulated: a) root-filled tooth with SF; b) root-filled tooth after removal of the SF by using MK, UT, or BP techniques. The models were loaded axially (from two directions) and vertically (300 N), and von Mises stresses were then analyzed. SFs increased the stresses within the root. Longer SFs cause higher stresses within the root and thus should be removed, while short SFs could be kept considering the other clinical factors. Removal via MK caused the highest stresses within the roots among the techniques used. Axial loading caused higher stresses at the cervical side, while the stresses moved toward the apical side under vertical loading. SFs increase the stresses within the root. Long SFs should be removed while short SFs can be left (considering other clinical factors that may affect the success of the treatment). Removing short SFs located at the apical side negatively affects the biomechanics of the teeth, and this effect is more dramatic with the MK technique.