Ever increasing complexity of systems has stimulated the development of sophisticated methods and tools for modeling and analysis of today‘s enterprises. Recent advances in information technology along with significant progress in analytical and computational techniques have facilitated the use of such methods and tools in industry. However, enterprise modeling and analysis methods are yet to make a significant impact on the decision-making processes of most companies and organizations. In this paper, we provide a detailed analysis of the major roadblocks to a broader use of enterprise modeling and analysis methods along with our methodical approach and a software implementation that addresses them.