RNA plays important roles in the regulation of gene expressions and other cellular functions. It functions as both as an informational carrier and a nanomachine due to its complementary base-pairing ability and complexed three-dimensional structure. Several nanostructures have been designed and constructed by exploiting these natural RNA properties. In this review, we will introduce the design principles of RNA nanostructures and their biotechnology applications as molecular scaffolds. RNA-based molecular scaffolds can control the accumulation and interaction of target proteins at nanometer-scale to regulate the function of bacterial and mammalian cells. Combining useful property of RNA as a nano-material and a molecular scaffold may provide us powerful tools in biological research, bioengineering, and future medicine.