The authors propose a protocol to derive finite element (FE) models from micro computer tomography scans of implanted rat bone. A semi-automatic procedure allows segmenting the images using specimen-specific bone mineral density (BMD) thresholds. An open-source FE model generator processes the segmented images to a quality tetrahedral mesh. The material properties assigned to each element are integrated from the BMD field. Piecewise, threshold-dependent density-elasticity relationships are implemented to limit the effects of metal artefacts. A detailed sensitivity study highlights the coherence of the generated models and quantifies the influence of the modelling parameters on the results. Two applications of the protocol are proposed. The stiffness of bare and implanted rat tibiae specimens is predicted by simulating three-point bending and inter-implant displacement, respectively. Results are compared with experimental tests. The mean value and the variability between the specimens are well captured in both tests.