In this chapter, we adopt the established model of network-of-networks to design optimal secure interdependent IoT-enabled infrastructures. IoT networks are vulnerable to cyber attacks which result in link removals. We develop a heterogeneous IoT network design framework in which a network designer can add links to provide additional communication paths between two nodes or secure links against attacks by investing resources. We characterize the optimal design strategy and then develop a method to construct networks that satisfy design specifications. Finally, we provide case studies on the Internet of Battlefield Things (IoBT) to illustrate the obtained results.