Single crystal semiconductors almost always exhibit better optoelectrical properties than their polycrystalline or amorphous counterparts. While three-dimensionally (3D) nanostructured semiconductor devices have been proposed for numerous applications, in the vast majority of reports, the semiconductor is polycrystalline or amorphous, greatly reducing the potential for advanced properties. While technologies for 3D structuring of semiconductors via use of a 3D template have advanced significantly, approaches for epitaxially growing nanostructured single crystal semiconductors within a template remain limited. Here, we demonstrate the epitaxial growth of 3D-structured ZnO through colloidal templates formed from 225 and 600 nm diameter colloidal particles via a low-temperature (∼80 °C) hydrothermal process using a flow reactor. The effects of the pH of the reaction solution as well as the additive used on the 3D epitaxy process are investigated. The optical and electrical properties of the epitaxially grown nanostructured ZnO are probed by reflectance, photoluminescence, and Hall effect measurements. It is found that the epitaxially grown nanostructured ZnO generally exhibits properties superior to those of polycrystalline ZnO. The demonstrated hydrothermal epitaxy process should be applicable to other chemical solution-based deposition techniques and help extend the range of materials that can be grown into a 3D nanostructured single-crystalline form.