We present a novel ion trap fabrication method enabling the realization of multilayer ion traps scalable to an in principle arbitrary number of metal-dielectric levels. We benchmark our method by fabricating a multilayer ion trap with integrated three-dimensional microwave circuitry. We demonstrate ion trapping and microwave control of the hyperfine states of a laser cooled (\,^{9})Be(^{+}) ion held at a distance of 35(\,\mu)m above the trap surface. This method can be used to implement large-scale ion trap arrays for scalable quantum information processing and quantum simulation.