mode-mitigation, as well as signal-routing, which are vital as quantum computers scale in qubit number, and thus dimension. High-coherence qubits are required to build fault-tolerant quantum computers and so material choices are an important consideration when developing a qubit technology platform. Sapphire, as a low-loss dielectric substrate, has shown to support high-coherence qubits. In addition, recent advances in material choices such as tantalum and titanium-nitride, both deposited on a sapphire substrate, have demonstrated qubit lifetimes exceeding 0.3 ms. However, the lack of any process equivalent of deep-silicon etching to create through-substrate-vias in sapphire, or to inductively shunt large dies, has limited sapphire to small-scale processors, or necessitates the use of chiplet architecture. Here, we present a sapphire machining process that is compatible with high-coherence qubits. This technique immediately provides a means to scale QPUs with integrated mode-mitigation, and provides a route toward the development of through-sapphire-vias, both of which allow the advantages of sapphire to be leveraged as well as facilitating the use of sapphire-compatible materials for large-scale QPUs.