Aim To evaluate the relative performance of FlexMaster nickel-titanium instruments shaping maxillary molar root canals in vitro. Methodology Extracted human maxillary molars were scanned, before and after root-canal shaping, with FlexMaster, employing micro-computed tomography (muCT) at a resolution of 36 mum. Canals were three-dimensionally reconstructed and evaluated for volume, surface area, 'thickness' (diameter), canal transportation and prepared surface. Based on median canal volume, the canals were divided into 'wide' and 'constricted' groups. Comparisons were made between mesiobuccal (mb), distobuccal (db) and palatal (p), as well as 'wide' and 'constricted' canals, using ANOVA and Scheffe post-hoc tests. Results Volume and surface area increased significantly and similarly in mb, db and p canals, and no gross preparation errors were found. Mean root-canal diameters, 5 mm coronal to the apex, increased from 0.45 to 0.65 mm, from 0.41 to 0.56 mm and from 0.79 to 0.85 mm for mb, db and p canals, respectively. Apical canal transportation ranged from 0.01 to 0.29 mm and was independent of canal type; 'wide' canals had a significantly higher (P < 0.05) proportion of unprepared surfaces than 'constricted' canals had. Conclusions FlexMaster instruments shaped curved and narrow root canals in maxillary molars to sizes 40 and 45 without significant shaping errors. Canal anatomy had an insignificant impact on preparation, indicating that FlexMaster instruments were able to shape 'constricted' canals as well as 'wide' ones.