In the recent years the rapid prototyping technology has become increasingly important as a manufacturing method for many medical devices. Although the advantage of such technology is evident, a precise presentation of the actual anatomical parts as well as shape accuracy and surface quality is a major indicator for choosing the best technique. In this paper, evaluation and validation of the shape accuracy of fabricated models using Fused Deposition Modelling technique is presented. The surface deviation between anatomical models (a mandible) derived from Computed Tomography and their virtual presentation was investigated. A high level of conformity with regard to the surface feature of the anatomical part was observed. Furthermore, surface deviations in the range of ±0.5 mm with an absolute mean deviation of 0.159 mm for the model were reported. The surface accuracies suggest that the reproduction of complex anatomical structures by FDM could potentially be used for surgical planning, custom-made implants and for surgical anatomy teaching.