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We describe the use of laser-enhanced etching of fused silica in order to build multilayer ion traps. This technique offers high precision of both machining and alignment of adjacent wafers. As examples of designs taking advantage of this possibility, we describe traps for realizing two key elements of scaling trapped ion systems. The first is a trap for a cavity-QED interface between single ions and photons, in which the fabrication allows shapes that provide good electrostatic shielding of the ion from charge buildup on the mirror surfaces. The second incorporates two X-junctions allowing two-dimensional shuttling of ions. Here, we are able to investigate designs which explore a trade-off between pseudopotential barriers and confinement at the junction center. In both cases, we illustrate the design constraints arising from the fabrication. [ABSTRACT FROM AUTHOR]