Commonly used boundary-based solid and surface modeling methods in traditional computer aided design are not capable of constructing configurations with large numbers of particles or complex topology. In this paper, we propose a new geometric modeling scheme, periodic surface, for material design at atomic, molecular, and meso scales. At molecular scale, periodicity of the model allows thousands of particles to be built efficiently. At meso scale, inherent porosity of the model represents morphology of polymer and macromolecule naturally. Model construction and operation methods are developed to build crystal and molecular models based on periodic surfaces.