In this paper, three types of microstructures are argued as substrates for electrochemical deposition of Au nanodots. They include: (a) aero-GaN consisting of hollow GaN microtetrapods, (b) microdomains of pores with a controlled design produced by anodization of InP wafers, and (c) patterned microdomains composed of strips with alternating electrical conductivity in GaN crystals grown by hydride vapor phase epitaxy. Uniform deposition of Au nanodots with controlled density is demonstrated by using pulsed electroplating, the voltage pulse width and amplitude as well as the pause between pulses and the conductivity of the substrate serving as adjustable parameters. The morphology of the produced hybrid microarchitectures was investigated by scanning electron microscopy. The explored microstructures are proposed as platforms for the development of complex 3D hybrid micro-nano-architectures via the vapor–liquid–solid deposition of various semiconductor nanowires with Au nanodots as catalysts.