We have developed a number of computational tools that permit a user to design RNA based nano-particles with various functionalities. One of these tools is a newly developed relational database, RNAJunction, which contains structural and sequence information for all known RNA n-way junctions and kissing loop interactions. The database also contains the results from applying molecular mechanics and structural clustering techniques to the motifs. The database of motifs can be searched in a variety of ways and provide a source for further analysis and RNA nano building blocks. Another computational tool, NanoTiler, permits a user to interactively and automatically construct user specified RNA-based nano-scale shapes. The combination of the RNAJunction database, NanoTiler and other computational tools allows the rapid prototyping of designed RNA shapes. We discuss some of the principles involved in these design tools and show how the RNA nanodesign process can be accomplished with the use of these methodologies.