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Robotic-assisted orthopaedic surgeries demand accurate, automated leg manipulation for improved spatial accuracy to reduce iatrogenic damage. In this study, we propose novel rigid body designs and an optical tracking volume setup for tracking of the femur, tibia and surgical instruments. Anatomical points inside the leg are measured using Computed Tomography with an accuracy of 0.3mm. Combined with kinematic modelling, we can express these points relative to any frame and across joints to sub-millimetre accuracy. It enables the setup of vectors on the mechanical axes of the femur and tibia for kinematic analysis. Cadaveric experiments are used to verify the tracking of internal anatomies and joint motion analysis. The proposed integrated solution is a first step in the automation of leg manipulation and can be used as a ground-truth for future robot-assisted orthopaedic research.