A large number of clusters are being used in all different organizations such as universities, laboratories, etc. These clusters are, however, usually independent from each other even in the same organization or building. To provide a single image of such clusters to users and utilize them in an integrated manner, cluster-of-clusters has been suggested. However, since research groups usually do not have the actual backbone networks for cluster-of-clusters, which can be reconfigured with respect to delay, packet loss, etc. as needed, it is not feasible to carry out practical research over realistic environments. Accordingly, the demand for an efficient way to emulate the backbone networks for cluster-of-clusters is overreaching. In this paper, we suggest a novel design for emulating the backbone networks of cluster-of-clusters. The emulator named NemC can support the fine-grained network delay resolution minimizing the additional overheads. The experimental results show that NemC can emulate the low delay and high bandwidth backbone networks more accurately than existing emulators such as NISTNet and NetEm. We also present a case study showing the performance of MPI applications over cluster-of-clusters environment using NemC.