Numerical modelling of the coronary tree is well established. Solutions of the Navier-Stokes equations can produce wall shear stress distributions which can be used to correlate the position of shear stress distribution with coronary artery disease. We have previously demonstrated a technique for reconstructing a single branch of the coronary tree. The introduction of junctions into the model allows for accurate reconstruction of potentially the entire arterial tree. However the introduction of a realistic junction has proven to be difficult. A four section method for branching has been adopted, utilising three tubular segments and a small junction section as the join. This allows for automatic generation of the majority of the artery (the tubes), and a semi-automated procedure concentrating specifically on the junction. A structured mesh is used for the tubes, allowing for easy generation and improved computation time, whilst an unstructured mesh is used to accurately model the irregular shape of the junction. The four section method allows for easy insertion of more branches, depending on the level of detail required. Another advantage is that as time evolves, inducing conformational changes throughout the cardiac cycle, the tubes can be regenerated, whilst the junction needs only slight modification. Marked changes are induced in wall shear stress by either adding extra junctions to an arterial tree, or altering the shape of major branches.