The purpose of this study was to compare the effects of preparation with GT files and profiles .04 in shaping of root canals and reconstruct the three-dimensional root canal system using micro computed tomography 40 canals of the extracted human mandibular molars were used, and randomly distributed into two experimental groups. In group 1. canals were prepared by GT files. In group 2, Profiles .04. were used. Apical preparation size was #30. For each tooth pre and post operative cross-sectional images were obtained by the micro CT at 50 micron intervals. Pre and post operative cross-sectional images of 1, 2, 3, 5, and 8mm from the apex were compared. For each section. canal area and centering ratio were determined. For each tooth pre- and post-operative root canal volume from the furcation to the apex of the roots was calculated by three-dimensional image software. Following results were obtained: 1. At 8mm from the apex, area of dentin removed by GT rotary file was significantly larger than that by Profile .04. And at the other levels there was not a significant difference. 2. There was a trend for GT rotary file to remain more centered in the canals than Profile .04 at all levels. But at 3mm level. there was a statistically significant difference. 3. In root canal volume increments after instrumentation, there was no significant difference between two groups.