Computational modelling is an invaluable tool for investigating features of human locomotion and motor control which cannot be measured except through invasive techniques. Recent research has focussed on creating personalised musculoskeletal models using population-based morphing or directly from medical imaging. Although progress has been made, robust definition of two critical model parameters remains challenging: (1) complete tibiofemoral (TF) and patellofemoral (PF) joint motions, and (2) muscle tendon unit (MTU) pathways and kinematics (i.e. lengths and moment arms). The aim of this study was to develop an automated framework, using population-based morphing approaches to create personalised musculoskeletal models, consisting of personalised bone geometries, TF and PF joint mechanisms, and MTU pathways and kinematics. Informed from medical imaging, personalised rigid body TF and PF joint mechanisms were created. Using atlas- and optimisation-based methods, personalised MTU pathways and kinematics were created with the aim of preventing MTU penetration into bones and achieving smooth MTU kinematics that follow patterns from existing literature. This framework was integrated into the Musculoskeletal Atlas Project Client software package to create and optimise models for 6 participants with incrementally increasing levels of personalisation with the aim of improving MTU kinematics and pathways. Three comparisons were made: (1) non-optimised (Model 1) and optimised models (Model 3) with generic joint mechanisms; (2) non-optimised (Model 2) and optimised models (Model 4) with personalised joint mechanisms; and (3) both optimised models (Model 3 and 4). Following optimisation, improvements were consistently shown in pattern similarity to cadaveric data in comparison (1) and (2). For comparison (3), a number of comparisons showed no significant difference between the two compared models. Importantly, optimisation did not produce statistically significantly worse results in any case.