Finite element modeling method (FEM) is a powerful numerical analysis method that is widely used in various engineering and scientific domains. In this thesis, we have utilized FEM to study structural analysis, heat transfer, and fluid flow in the instrumentation design and optimization. In particular, we have designed and optimized a portable micro-dispenser for bio-medical applications and a portable enclosure device for industrial applications. In the micro-dispenser study, our proposed model is comprised of a permanent mainframe and a disposable main tank, which can hold a bulk volume of sample fluid as an off-chip reservoir. The height of the micro-dispenser and the diameter of the passive valve have been analytically designed upon the...