We demonstrate immobilization of DNA nanostructures (37 nm × 8 nm) on silicon by a combination of “top-down” fabrication and “bottom-up” self-assembly. Anchor lines and pads were defined using electron beam lithography and a cationic molecular monolayer. Individual DNA nanostructures bind in 85% yield onto the anchor pads and can be washed and imaged in air. The strength of the binding interaction between a DNA nanostructure and its anchor pad is at least −43 kJ/mol.