Some fundamental aspects of the three-level (micro-, meso-, and macrolevel) scheme of modeling nanomaterial structure based on physics of quantum-sized mesoparticles are considered. Within the framework of quantum-field chemistry, the mesoparticles provide the basis for the construction of mesoquanta and macrodefects of nanomaterials. The microstructure is described by the method of quantum density topology, and the macrostructure is described by the method of thermal field dynamics of quantum-sized mesoparticles. Based on an analysis of quantum-sized nanoparticle motion, a strict mathematical classification of physical and chemical mesoprocesses in nanomaterials is given.