Experimental quantum information processing with superconducting circuits is rapidly advancing, driven by innovation in two classes of devices, one involving planar micro-fabricated (2D) resonators, and the other involving machined three-dimensional (3D) cavities. We demonstrate that circuit quantum electrodynamics can be implemented in a multilayer superconducting structure that combines 2D and 3D advantages. We employ standard micro-fabrication techniques to pattern each layer, and rely on a vacuum gap between the layers to store the electromagnetic energy. Planar qubits are lithographically defined as an aperture in a conducting boundary of the resonators. We demonstrate the aperture concept by implementing an integrated, two cavity-modes, one transmon-qubit system.