A comparison of the preparation ability of two root canal instrumentation systems in oval-shaped canals using micro-computed tomography was undertaken. Thirty extracted, single-rooted, human mandibular premolars with radiographically similar canal morphology were selected, allocated to two groups (N = 15) and prepared with TRUShape or Vortex Blue (VB). Each sample was subjected to three scans (20 lm resolution): pre-preparation and after preparation to sizes #30 and #40. Three-dimensional data sets were evaluated for canal volume, surface area and surface treatment. Matched axial slices in apical, middle and coronal root thirds were evaluated for cross-sectional area, roundness and transportation. Preparation with both instruments increased canal volumes and surface areas similarly and significantly (P < 0.001) with no significant difference between groups. TRUShape significantly enhanced surface treatment at both apical sizes (P < 0.05). Transportation exceeded 100 lm in only eight out of 90 cross sections. Both instruments performed similarly during preparation. TRUShape, however, significantly enhanced surface treatment.