Graphene, the one-atom-thick sp 2 -hybridized carbon crystal, displays unique electronic, structural and mechanical properties, which promise a large number of interesting applications in diverse high-tech fields. Many of these applications require its functionalization, e.g., with substitution of carbon atoms or adhesion of chemical species, creation of defects, modification of structure or morphology, to open an electronic band gap to use it in electronics, or to create 3D frameworks for volumetric applications. Understanding the morphology-properties relationship is the first step to efficiently functionalize graphene. Therefore, a great theoretical effort has been recently devoted to model graphene in different conditions and with different approaches involving different levels of accuracy and resolution. Here, we review the modeling approaches to graphene systems, with a special focus on atomistic level methods, but extending our analysis onto coarser scales. We illustrate the methods by means of applications with possible potential impact.