MoleculeCrafter is a novel tool that facilitates the custom creation of flexible and modular macromolecular model kits. These models support student chemical education by providing a manipulable and visuospatial tool to facilitate exploration of chemical structures and their interactions. Here, for the first time, we demonstrate using MoleculeCrafter for the creation of flexible and modular nucleic acid models capable of undergoing the noncanonical base pairing found in RNA structures as well as DNA triplex and quadruplex structures. While flexible models of DNA and peptide nucleic acid (PNA) have previously been created, they typically enable only one method of bonding, namely, Watson-Crick-Franklin base pairing. This tool provides an engaging demonstration of how MoleculeCrafter can be leveraged to make complex models showcasing new features such as bases that can bind at their Watson-Crick-Franklin, Hoogsteen, and Sugar edges. To go further and enable users to create their custom molecular model kits, we have designed a workflow for extracting atomic position data for use with our novel CAD tool, which can generate molecular model kits from data files, affix predesigned connectors, and align and label parts for production via 3D printing. We tested our tool by modeling, printing, and assembling four structures, ultimately demonstrating MoleculeCrafter's efficacy as a tool for designing customized flexible and articulated molecules.