Low-cost and robust platforms are key for the development of next-generation 3D micro- and nanodevices. To fabricate such platforms, nanocrystalline diamond (NCD) is a highly appealing material due to its biocompatibility, robustness, and mechanical, electrical, electrochemical, and optical properties, while glass substrates with through vias are ideal interposers for 3D integration due to the excellent properties of glass. A low-cost process—free of photolithography and transfer printing—for fabricating arrays of TGVs that are sealed with suspended portions of an ultra-thin NCD film on one side is presented. These highly transparent structures may serve as a platform for the development of microwells for single-cell culture and analysis, 3D integrated devices such as microelectrodes, and quantum technologies. It is also possible to replace the NCD with silicon nitride or silicon carbide, allowing for the development of complex heterogeneous structures on a small scale.