Fluorescence signals of quantum dots (QDs) influenced by different array structures of gold-coated silicon nanorods (SiNRs) were investigated via experimental observations and two-dimensional (2D) finite element method (FEM) simulations. On the densest gold-coated SiNRs array structure, the highest QD fluorescence quenching rates were observed and on the sparsest array structure, the highest QD fluorescence enhancement rates were observed. By developing a new technique which obtains the optical image of the array structures without losing information about the QD locations, we were able to further investigate how the QD fluorescence is influenced by spatially controlled array structures.