Multi-height metallic structures are of importance for various MEMS applications, including master molds for creating 3D structures by nanoimprint lithography, or realizing vertically displaced electrodes for out-of-plane electrostatic actuators. Normally these types of multi-height structures require a multi-mask process with increased fabrication complexity. In this work, a fabrication technology is presented in which fully-isolated, dual-height MEMS metallic structures separated by narrow gaps can be realized using a self-aligned, single-mask process. The main scheme of this proposed process is through-mold electrodeposition, where two photoresist mold fabrication steps and two electrodeposition steps are sequentially implemented to define the thinner and thicker structures in the dual-height configuration. The process relies on two selfaligned steps enabled by the electrodeposited thinner structures: a wet-etching of the seed layer utilizing the thinner structure as an etch-mask to electrically isolate the thinner and the thicker structures, and a backside UV lithography utilizing the thinner structure as a lithographic mask to create a high-aspect-ratio mold for the thicker structure through-mold electrodeposition. The latter step requires the metallic structures to be fabricated on a transparent substrate. Test structures with differences in aspect ratio are demonstrated to showcase the capability of the process.