A method to simulate contact between two boundaries of structures which are not aligned to predefined axes when using Comsol Multi-physics (v3.3, Comsol Ltd, Cambridge, UK) is presented. This method was developed because of limitations in the existing default contact modelling. Some of these limitations were recently addressed in a separate study; however, the method exploited symmetry across an axis of the coordinate system. The method presented here enables contact modelling with arbitrarily aligned structures within such a coordinate system. The contact method presented is then applied to a simple model with two deformable structures that come into contact, and compared over a range of positions. Results show a minimal variation in peak stress and contact pressure with model orientation, demonstrating that results are independent of orientation. Therefore, the contact method enables contact simulations in Comsol Multi-physics without assuming symmetry about an axis for contract. The method is compatible with the true transient contact method defined.