A self-aligned tunable metamaterial is formed as a wire mesh. Self-aligned channel grids are formed in layers in a silicon substrate using deep trench formation and a high-temperature anneal. Vertical wells at the channels may also be etched. This may result in a three-dimensional mesh grid of metal and other material. In another embodiment, metallic beads are deposited at each intersection of the mesh grid, the grid is encased in a rigid medium, and the mesh grid is removed to form an artificial nanocrystal.