In this report, we introduce a method utilizing ion-assisted aerosol lithography to stack 3D nanostructures vertically. The stacked 3D nanostructures exhibit extraordinary optical properties: the double layer 3D nanostructures show more than 5-fold increased surface enhanced Raman scattering intensities compared to their single layer counterpart. This unusual enhancement of Raman intensity implies the existence of additional vertical hotspots formed by interlayer cavity effects between the lower and upper nanostructures. Allowing for full three-dimensional control in nanofabrication, this work provides a reliable way to create complex-shaped advanced optical nanostructures with non-intuitive bulk optical properties.