In Japan, regional cluster policies are recognized as intensive projects to form effective knowledge networks. On the other hand, the methodology to evaluate these network structures is still under development. This paper clarifies that scope of the area significantly affects the evaluation of regional network structure by using network analysis. First of all, this paper evaluates an inter-firm network of Nagano prefecture in Kanto area by using trade data which includes 27,418 companies and 70,725 trades in Kanto area. Secondly, inter-firm network within Nagano is evaluated by using data which includes 1,309 companies in Nagano prefecture. Finally, this paper divides the Nagano network into four economic blocks and compares them. Inter-firm network in Nagano is comparatively evaluated a closed in Kanto area. On the other hand, the network within Nagano prefecture in its self has a small-world topology. Moreover, there is clear difference among the four economic blocks in each other connections. This paper concludes that there is a great reliance on the setup of the geographical boundary when evaluating the network structure. Our multi-layer analysis can contribute to the appropriate evaluation of network.