A novel, highly uniform and tunable hybrid plasmonic array is created via ion-milling, catalytic wet-etching and electron-beam evaporation, using a holographically featured structure as a milling mask. A simple and low-cost prism holographic lithography (HL) technique is applied to create an unprecedentedly coordinated array of elliptic gold (Au) holes, which act as the silicon (Si) etching catalyst in the reaction solution used to fabricate an elliptic silicon nanowire (SiNW) array; here, the SiNWs are arrayed hierarchically in such a way that three SiNWs are triangularly coordinated, and the triangles are arranged hexagonally. After removing the polymeric mask and metal thin film, the highly anisotropic thick Au film is deposited on the SiNW arrays. This hybrid substrate shows tunable optical properties in the near-infrared (NIR) region from 875 nm to 1030 nm and surface-enhanced Raman scattering (SERS) activities; these characteristics depend on the catalytic wet etching time, which changes the size of the vertical gap between the Au thick films deposited separately on the SiNWs. In addition, lateral interparticle coupling induces highly intensified SERS signals with good homogeneity. Finally, the Au-capped elliptical SiNW arrays can be hierarchically patterned by combining prism HL and conventional photolithography, and the highly enhanced fluorescence intensity associated with both the structural effects and the plasmon resonances is investigated.