We report on the structural and vibrational characterization of silicon (Si) nanowire arrays synthesized by metal-assisted chemical etching (MACE) of Si deposited with metal nanoparticles. Gold (Au) and silver (Ag) metal nanoparticles were synthesized by glancing angle deposition, and MACE was performed in a mixture of H2O2 and HF solution. We studied the structural differences between Au and Ag-etched Si nanowires. The morphology of the synthesized nanowires was characterized by scanning electron microscopy and transmission electron microscopy. The optical and vibrational properties of the Si nanostructures were studied by photoluminescence and Raman spectroscopy using three different excitation sources (UV, visible, and near-infrared) and are correlated to their microstructures. The structural differences between Au-etched and Ag-etched nanowires are due to the higher degree of hole injection by the Au nanoparticle and diffusion into the Si nanowires, causing enhanced Si etching by HF on the nanowire surface. Au-etched nanowires were observed to be mesoporous throughout the nanowire while Ag-etched nanowires consisted of a thin porous layer around the crystalline core. In addition, the surface-enhanced resonant Raman scattering observed is attributed to the presence of the sunken metal nanoparticles. Such Si nanostructures may be useful for a wide range of applications such as photovoltaic and biological and chemical sensing.