Computational analysis of trabecular bone normally involves the modeling of (experimental tests of) cored samples. However, the lack of constraint on the sides of the extracted trabecular bone samples limits the information that can be inferred regarding true in situ behavior. Here, the element-by-element voxel-based finite element method was applied via, a custom-written software suite (FEEBE), to a 72 μm resolution model of an ovine vertebra. The difference between the apparent modulus of eight concentric core cylinders when modeled as part of the whole bone (containing 84 × 106 degrees of freedom) and independent of the whole bone was investigated. The results showed that cored trabecular bone apparent modulus depended significantly on the core diameter when modeled as an extracted core (r² = 0.975) and as part of a whole bone (r² = 0.986). The cause of this result was separated into the side-artifact effect and bone volume fraction (BV/TV) effect. For the independently modeled cores, the apparent modulus of an inner core region of interest varied with increasing thickness of the outer annulus. This was attributed to the side-artifact effect, given that the BV/TV of the core region was constant. Within the whole trabecular structure, the side artifact was eliminated as the entire bone structure was modeled. However, a BV/TV effect influenced the apparent modulus depending on the size of the core selected for determining apparent modulus. Changing the size of the core varied the overall BV/TV of the core, and this significantly (r² = 0.999) influences the apparent modulus. Therefore, determining a ‘true’ apparent modulus for trabecular bone was not achievable. The independently modeled cores consistently under-predict the in vivo apparent modulus. It is recommended that if a ‘true’ apparent modulus is required, the BV/TV at which it is required needs to be first determined. Apparent modeling of entire bones at microscale resolution allowed regions of low and high tissue strains to be identified, consistent with patterns of trabecular bone remodeling and resorption reported in literature. The basivertebral vein cavity underwent the highest strains within the entire vertebral body, suggesting that failure might initiate here, despite containing visibly thicker struts and plate trabeculae. Although computationally expensive, analysis of the entire vertebral body provided a full picture of in situ trabecular bone deformation.