Many complex systems, such as software systems, are full of complexity arising from interactions among basic units (such as classes, interfaces and struts in object-oriented software systems). One of the most successful approaches to capture the underlying structural features of large-scale software systems is the investigation of hierarchical organization. However, the hierarchy of software networks has not been thoroughly investigated. In this paper, the crucial fraction (CF) in software networks has been extracted and analyzed in a set of real-world software systems. First, the classes and the relationships between them have been extracted into software networks. Then software networks have been divided into different layers, and CF of software networks has been extracted by k-core. The empirical studies in this paper reveal that software networks represent flat hierarchical structure. Finally, CF has been measured by the relevant complex network parameters respectively, and the relations between CF and overall network have been analyzed by the case studies of software networks. The results show that CF represents characteristics of scale-free, small-world, strong connectivity, and the units in CF are frequently reused and dominate the overall system.