Mitigating lightning Direct Effects (DE) damage on aerospace vehicles is an important engineering challenge and is directly related to safety of flight. Depending on the threat level and materials involved, vehicle surfaces and other design features may need to be protected to help mitigate damage. Numerical simulation can provide insight into the amount of damage likely to occur during a lightning strike and can reduce the costs associated with an expensive testing program. We here present a new simulation tool for such analyses that we believe provides unique capabilities especially well-suited for the protection of aerospace platforms, and we apply this new tool to the analysis of lightning DE on an anisotropic composite surface. Our simulation tool is the combined framework of EMA3D and the Elmer thermal physics solver. This new analysis platform allows for the correct description of anisotropic materials at both the electrical and thermal level. By implementing DE analysis capabilities in EMA3D we find a comprehensive avenue through which to analyse a wide range of E3 concerns for an entire aerospace vehicle.