The finite element (FE) method was originally developed on a physical basis for the computation of structure-mechanical problems. Meanwhile, it has been widely applied to medical issues. This study sought a suitable method to build a FE model for remodelling processes in osseous defects supplemented with bone substitute material. For this purpose, the second right premolars were extracted from four pig mandibles (Sus scrofa domesticus) and the extraction alveoli were provided with synthetic bone substitute material. After 70 days, a segmented osteotomy of this area was performed for specimen collection. Radiographs of the specimens were taken in defined planes before and after fixation and embedded with Technovit 9100. Fixation-related shrinkage was quantified from the radiographs using reference lines. Computer tomographic (CT) and microCT images of the fixed and embedded specimens were obtained. From these data, a FE model was built. The construction of a FE model is sufficient to represent bone remodelling after supply of bone substitute material. The use of microCT data permits building a clearly more precise model.