This paper presents the high performance software to enables scientific researchers for predicting, visualizing and observing the temperature behavior and some parameter characteristics of nanoscale multilayer full chip system and nanowire fabrication. The analysis of scientific algorithms and high performance computing are searchable through a user friendly web-based system. This software will involve some mathematical modeling, numerical simulations and high performance computing technology to improve the accuracy of prediction, visualization quality and parallel performance indicators. The parameters characterization of multilayer full chip system and nanowire fabrication will focus on temperature behavior, electromagnetic wave motion, density distribution, heat spreader and heat sink. The implementations of parallel algorithms for solving the Partial Differential Equation for heat transfer and wave motion problems are based on large sparse parabolic and elliptic types. The discretization technique to obtain a large sparse linear system of equations is based on Finite Difference Method. The SCLP software will support the high performance computing of numerical simulations and its repository using distributed memory architecture. The performance indicators will investigate the parallel programs using Parallel Virtual Machine (PVM) and C language on Linux operating system in terms of run time, accuracy, convergence, errors, speedup, efficiency and effectiveness. As a conclusion, high performance software will be an alternative software system to support huge computational complexity of multilayer nanochip system and nanowire fabrication model.