Minimally invasive surgeries aiming to restore fractured vertebral body are increasing; therefore, our goals were to create a 3D vertebra reconstruction process and design clinical indices to assess the vertebral restoration in terms of heights, angles and volumes. Based on computed tomography (CT)-scan of the vertebral spine, a 3D reconstruction method as well as relevant clinical indices were developed. First, a vertebra initial solution requiring 5 min of manual adjustments is built. Then an image processing algorithm places this solution in the CT-scan images volume to adjust the model's nodes. On the vertebral body's anterior and posterior parts, nine robust heights, volume and endplate angle measurement methods were developed. These parameters were evaluated by reproducibility and accuracy studies. The vertebral body reconstruction accuracy was 1.0 mm; heights and volume accuracy were, respectively, 1.2 and 179 mm3. In conclusion, a 3D vertebra reconstruction process requiring little user time was proposed as well as 3D clinical indices assessing fractured and restored vertebra.