High-level Petri nets are a powerful formal method for modeling and analyzing systems; however their applications are mainly limited to small-scale research projects due to a lack of modularity and hierarchy within the formalism itself and a systematic approach in using the formalism. In our previous work, a methodology for constructing hierarchical and structured high-level Petri net specifications has been developed. In this paper, we further explore and refine our methodology for using hierarchical high-level Petri nets in systems analysis. Our new approach has adapted the mature results from the Data Flow Diagram method and is demonstrated through a library system.