as control wires, qubits, and resonators between multiple layers. The frequencies of resonators and qubits in flip-chip-bonded multi-chip modules depend on the details of their electromagnetic environment defined by the conductors and dielectrics in their vicinity. Accurate frequency targeting therefore requires precise control of the separation between chips and minimization of their relative tilt. Here, we describe a method to control the inter-chip separation by using polymer spacers. Compared to an identical process without spacers, we reduce the measured planarity error by a factor of 3.5, to a mean tilt of 76(35) μrad, and the deviation from the target inter-chip separation by a factor of ten, to a mean of 0.4(8) μm. We apply this process to coplanar waveguide resonator samples and observe chip-to-chip resonator frequency variations below 50 MHz (≈ 1 %). We measure internal quality factors of 5×105 at the single-photon level, suggesting that the added spacers are compatible with low-loss device fabrication.