Background: Patient specific 3D modeling is the first step towards image-guided surgery, the actual revolution in surgical care. Pediatric and adolescent patients with rare tumors and malformations should highly benefit from these latest technological innovations, allowing personalized tailored surgery. This study focused on the pelvic region, located at the crossroads of the urinary, digestive and genital channels with important vascular and nervous structures. The aim of this study was to evaluate the performances of different software tools to obtain patient specific 3D models, through segmentation of magnetic resonance images (MRI), the reference for pediatric pelvis examination. Methods: Twelve software tools freely available on the Internet and two commercial software tools were evaluated using T2-w MRI and diffusion- weighted MRI images. The software tools were rated accordingly to eight criteria, evaluated by three different users: automatization degree, segmentation time, usability, 3D visualization, presence of image registration tools, tractography tools, supported OS, and potential extension (i.e. plugins). Results: A ranking of software tools for 3D modeling of MRI medical images, according to the set of predefined criteria, was given. This ranking allowed us to elaborate guidelines for the choice of software tools for pelvic surgical planning in pediatric patients. The best-ranked software tools were Myrian Studio, ITK-SNAP and 3D Slicer, the latter being especially appropriate if nerve fibers should be included in the 3D patient model. Conclusion: This study proposed a comprehensive review of software tools for 3D modeling of the pelvis according to a set of eight criteria, and delivered specific conclusions for pediatric and adolescent patients that can be directly applied to clinical practice.