Bone anchored amputation prostheses connect a persons amputated limb to an artificial limb. They are surgically implanted as an alternative to a prosthetic socket. This paper reports on the use of computer simulations to analyse how varying two measurements can affect stresses in the implant. These measurements were firstly, thickness of the bone wall into which the implant sits and secondly, the shape of the threads along the screw part of the implant. Varying both measurements had an effect on the implant stress and the conclusion was that this could guide future implant design optimisation.