A method and system for fabricating nano-scale structures, such as channels (i.e., nano-channels) or vias (i.e., nano-vias. An open nano-structure, is formed in a substrate. Thereafter, an optional conformal material film may be deposited within and over the nano-structure using a first deposition process condition, and then the open nano-structure is closed off to form a closed nano-structure using a second deposition process condition, including one or more process steps.