Label-free optical biochemical analysis approach is an advantageous alternative to traditional label-based techniques and has a wide range of applications. Extraordinary optical transmission (EDT), another form of surface plasmonic resonance induced by sub-wavelength nanopore arrays, has recently drawn increasing attention, due to its potential in miniaturizing biochemical assay instrument. To fabricate the nanopore arrays that function as the core device for biochemical analysis, the parameters are to be determined in an optimized manner. This paper thus reports the simulation studies on two typical structures of nanopore arrays, namely, (A) a perforated metallic layer on top of a substrate, and (B) a perforated metallic layer coupled with isolated metallic disks, which have been proposed in literature. Using FDTD Solutions software, and taking into account the major factors associated with the transmitted light spectrum and intensity, this study confirms the importance of using coating on the nanopore arrays with a refractive index matching the substrate of nanopores. The simulation results also provide a quantitative comparison in performance of the structures with different parameters, in terms of spectrum shift and intensity. These data can be used to guide the optimal design of a nanopores-based optical biochemical analyzer.