A process of creating controlled silver nanostructures using atomic force microscope technique is reported. The nanostructures are grown on both the silica surface and silica–indium-tin-oxide interface of a silver salt impregnated mesoporous silica film, deposited on indium tin oxide coated glass substrate. Voltage is applied between a conductive atomic force microscope tip and the indium tin oxide substrate to create the silver nanostructures. The possibility of switching the positions of the nanostructures between the silica film surface and the film–indium-tin-oxide interface, by reversing the electrical polarity of the tip, is demonstrated. It is also shown that the conductive channels can be created through the silica layer provided that the created metallic nanostructures are large enough to grow inside the film volume from one side to the other. The electrical conductivity of the film can be locally changed in a reversible manner by applying successively negative and positive voltages to the tip.