Heterotopic ossification (HO) is the process of bone formation in tissues that are not usually osseous. It occurs in 60% of those with blast-related amputations. HO can result in reduced range of motion, pain, nerve impingement and can affect prosthesis fitting and is caused by a combination of mechanical, biological, local and systemic factors. As with normal bone formation and remodelling, it is expected that heterotopic bone responds to mechanical stimuli and understanding this relationship can give insight into the pathology. The objective of this research was to investigate whether a physiological 2D computational model that considers both mechanical and biological factors can be used to simulate HO in the residual limb of a trans-femoral amputee. The study found that characteristic morphologies of HO were reproduced by adjusting the loading environment. Significant effects were produced by changing the loading direction on the femur; this is potentially associated with different initial surgical interventions such as muscle myodesis. Also, initial treatment such as negative pressure through a dressing was found to change the shape of heterotopic bone.