The control of nanoparticle synthesis using thermal plasmas is difficult and often leads to problems of chemical and structural purity, and poor process robustness in terms of consistency of product from run to run. Good reactor design allowed to overcome these issues and to develop a new material based on graphene with a flake-like structure (labeled graphene nanoflakes, GNF) supporting nitrogen for catalytic applications, for example as platinum replacement in fuel cells. These structures showed not only to be active, but also stable in polymer electrolyte fuel cell operation. Characterization of these structures, in situ fuel cell studies and modeling analysis all indicate that achievement of stability relates on the crystalline two-dimensional graphene structure. This paper first reviews the basic aspects behind the structural objectives, describes the synthesis process design leading to this crystalline structure, and provides a two-dimensional analysis on the graphitic growth based on fundamental theory and CFD calculations. These calculations indicate that an independent control of the graphene structure thickness (number of atomic planes) and sheet lengths is possible in a thermal plasma reactor.