Here, we report the fabrication and characterization of single crystal diamond films on a two-inch wafer-scale containing three-dimensional layered structures of negatively charged nitrogen-vacancy color centers (NV⁻). The (100)-oriented layered diamond films were grown by chemical vapor deposition (CVD) to create spatially separated regions of enhanced emission associated with NV⁻ centers. Such localized emission enhancement as well as 2D and 3D arrays of spins could enable close-packed architectures for emerging quantum devices, such as data processors, memory cells, and magnetic sensors. A cyclic sequence of CVD growth and oxygen-plasma etching is employed, resulting in the in-situ formation of layered inverted pyramidal structures with flat {111} sidewalls. These pits are subsequently overgrown by nitrogen-doped diamond to achieve NV⁻-rich facets with a uniform N-V bond arrangement and improved nitrogen incorporation efficiency.