In the present study, changes of morphologies and mechanical characteristics in the lumbar vertebrae of the ovariectomised (OVX) rats were investigated and analyzed by Finite Element (FE) and Rapid-Prototyped (RP) models based on micro-computed tomography (micro-CT). In previous researches, there were many studies about morphology such as bone mineral density and trabecular microstructure. However, detecting and tracking local changes were few in the trabecular and cortical bone of the lumbar vertebrae for the OVX rats. Experimental and simulated studies were used to investigate mechanical characteristics of the lumbar vertebral bones for the OVX rats. Three dimensional (3D) geometries of the models (RP and FE models), generated from in-vivo micro-CT scan data, were obtained from the 4th lumbar of the OVX rats. Three specimens (whole vertebral, trabecular and cortical bone models) were generated and analyzed in the simulated compression tests. For further verification, the experimental compression test for RP models ‘instead of real bone specimens’ was performed to indirectly validate the results of the simulated compression test for the FE models. The results were similar to those of the compression test simulated by micro-FE analysis. The present study showed the efficiency of the combined method (FE and RP techniques based on in-vivo micro-CT) as a nondestructive evaluation.