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Graph-based data representation is very popular in many research areas, including the field of cybersecurity, in which the community uses the so-called attacks graphs to model the cyber attacks since mid 90'. However, with the increasing complexity of cyber attacks and the protected systems, the attack models are growing and becoming complex networks. In this talk, we will show how complex networks can be used to model the protected systems (including large networks and infrastructures) and how they help in proactive and reactive cyber defense. We will go through several existing approaches and tools (e.g., CyGraph by MITRE, CRUSOE by CSIRT-MU) and discuss the challenges related to the everchanging threat landscape, insufficient or incompatible ontologies, and heterogeneity and frequent unavailability of relevant cybersecurity data that complicate the mining and other advanced analyses.