Advancements in computational power and micro-imaging has allowed the creation of finite element (FE) models on a microstructural level that can represent complex skeletal structures. These µFE models can analyze the structural integrity of individual trabeculae and may be used to model the impact of complex pathologies on skeletal stability. This thesis aims to:​ 1) optimize the histological identification of microdamage in healthy and mixed metastatic whole rat vertebrae, 2) quantify trabecular level stress and strain using µFE models and deformable registration generated from µCT data and 3) evaluate stress and strain in µFE models comparing undamaged regions with areas of mechanically induced microdamage. This novel technique allows the histological identification of microdamage in whole vertebrae with accurate alignment to 3D µCT data sets. In the µFE models, significantly higher stresses and strains were found in areas of damaged bone in both healthy and metastatically involved vertebrae.