In this paper the modeling aspects of some proposals of MEMS elements of fuel cells are explained. The necessity of a nonporous membrane, MEMS based pumps, anodes etc. has been eminent in recent fuel cells. The need for MEMS based models for porous silicon based membranes based on nano imprints technology has been met by modeling it in SUGAR in MATLAB environment. We have identified and categorized the domains of Nano enabled solar cells and have put forth a proposition for multi scale modeling of Solar cells. Multi scale modeling on HPC (High performance computing) of a Nano enabled solar cell is shown under MCCS (Microsoft compute cluster environment) environment using extreme optimization numerical library. Distribution and performance analysis of four levels of computation in a multi scale model is implemented with the distribution being carried out from classical semi-conductor to quantum levels as to accurately predict the behavior and properties of the solar cell.