We present a method for spatially selective immobilization of functional materials, such as proteins and nanoparticles, onto pre-activated silicon surfaces by electrochemical reaction. Carboxymethylbenzendiazonium (CMBD) cations, being adsorbable on silicon surfaces through electrochemically reductive deposition, is used as an anchor molecule to prepare the pre-activated silicon surfaces. It is demonstrated that the use of BD reaction is very efficient for the selective immobilization because the functional materials are immobilized exclusively onto the pre-adsorbed CMBD region. The method is applied to immobilize gold nanoparticles on the selected nanowire of the nanowire array.