The aim of this study was to evaluate root canals instrumented by dental students using the modified double-flared technique, nickel-titanium (NiTi) rotary System GT files and NiTi rotary ProTaper files by micro-computed tomography (MCT). A total of 36 root canals from 18 mesial roots of mandibular molar teeth were prepared; 12 canals were prepared with the modified double-flared technique, using K-flexofiles and Gates-Glidden burs; 12 canals were prepared using System GT and 12 using ProTaper rotary files. Each root was scanned using MCT preoperatively and postoperatively. At the coronal and mid-root sections, System GT and ProTaper files produced significantly less enlarged canal cross-sectional area, volume and perimeter than the modified double-flared technique (P < 0.05). In the mid-root sections there was significantly less thinning of the root structure towards the furcation with System GT and ProTaper (P < 0.05). The rotary techniques were both three times faster than the modified double-flared technique (P < 0.05). Qualitative evaluation of the preparations showed that both ProTaper and System GT were able to prepare root canals with little or no procedural error compared with the modified double-flared technique. Under the conditions of this study, inexperienced dental students were able to prepare curved root canals with rotary files with greater preservation of tooth structure, low risk of procedural errors and much quicker than with hand instruments.