In this paper we discuss the advanced methods for the stochastic process simulation at the atomic resolution, showing how they can achieve accurate predictions of the functionalization kinetics in multiple time and length scales. Focusing on processing of graphene based systems, the ingredients of the numerical method are highlighted: ab-initio study of key configurations stability, ”on lattice” matching of the energetic-configuration relationship, super-lattice and parallel-lattice formulation of complex kinetics, accelerate algorithms. Several examples of applications to graphene synthesis and manipulation processes are presented. Finally, we demonstrate that the fully potential of the technique is achieved when optical, magnetic and electronic properties of the simulated atomic configurations are analyzed by quantum mechanics based methods.