The use of computer-aided learning in education can be advantageous, especially when interactive 3D models are used to aid learning of complex 3-dimensional structures. The anatomy of the cerebral ventricular system is difficult to fully understand as it is seldom seen in 3D, as is the flow of cerebrospinal fluid (CSF). Using MR images of the ventricular system of the brain and several widely available commercial and free software packages, the techniques of 3D modelling, texturing, sculpting, image editing and animations were combined to create a workflow for the creation of an interactive education and training application. This was focussed on cerebral ventricular system anatomy and the flow of CSF. A robust methodology was produced, resulting in an interactive learning application detailing the anatomy of the cerebral ventricles and flow of CSF, using an anatomically accurate 3D model. The workflow presented shows how tutorials, animations and self-assessment tools can also be embedded into the training application. This study showed that an interactive educational and training package could be created for both specialist and non-specialist users, aiding understanding of an otherwise complex area of anatomy. This workflow methodology could be applied to other complex areas of anatomy to aid understanding.