Atomic, electronic structure and composition of top-down metal-assisted wet-chemically etched silicon nanowires were studied by synchrotron radiation based X-ray absorption near edge structure technique. Local surrounding of the silicon and oxygen atoms in silicon nanowires array was studied on as-prepared nanostructured surfaces (atop part of nanowires) and their bulk part after, first time applied, in-situ mechanical removal atop part of the formed silicon nanowires. Silicon suboxides together with disturbed silicon dioxide were found in the composition of the formed arrays that affects the electronic structure of silicon nanowires. The results obtained by us convincingly testify to the homogeneity of the phase composition of the side walls of silicon nanowires and the electronic structure in the entire length of the nanowire. The controlled formation of the silicon nanowires array may lead to smart engineering of its atomic and electronic structure that influences the exploiting strategy of metal-assisted wet-chemically etched silicon nanowires as universal matrices for different applications.