As designs for superconducting qubits become more complex, 3D integration of two or more vertically bonded chips will become necessary to enable increased density and connectivity.Precise control of the spacing between these chips is required for accurate prediction of circuit performance. In this paper, we demonstrate an improvement in the planarity of bonded superconducting qubit chips while retaining device performance by utilizing hard-stop silicon spacer posts. These silicon spacers are defined by etching several microns into a silicon substrate and are compatible with 3D-integrated qubit fabrication. This includes fabrication of Josephson junctions, superconducting air-bridge crossovers, underbump metallization and indium bumps. To qualify the integrated process, we demonstrate high-quality factor resonators on the etched surface and measure qubit coherence (T1, T2,echo > 40 {\mu}s) in the presence of silicon posts as near as 350 {\mu}m to the qubit.