If I understand your question correctly: This is a mechanical CAD task- a combination of reverse-engineering the parts of scan bodies you like from careful measurements, augmented with your own original work with a CAD suite (Solidworks, Fusion 360, Alibre, etc) to build a design that improves on or modifies the original. CAD design is its own skillset you have to learn, but it's a very useful one, especially if you have 3D printers you can use to instantly produce your design into a functional part.
Once you have your design, you just have to insert it into the library you're working with, which can be tricky; 3Shape's library builds assemblies out of modular parts, so even if you have a single design you like, you need to break it down to its constituent components to be able to work with it like any other component. In addition, it handles subtleties like fit-up for mating parts in its own way, so you have to design parts as per the system they use, and not what you'd normally use for part design; normally I'd design parts to have the clearances and final dimensions I'd, you know, want to end up with, but 3Shape handles that itself, so you give it a nominally-sized part with no clearance, and it adds the clearance itself by scaling the male mating parts (pins, mostly) down in X/Y.
Not a scan body, but close enough; I designed a custom articulator for our in-house use, because we liked some aspects of a SnowRock design, and other aspects of a Baumann, but didn't like their individual shortcomings. So I pulled all the dimensions off of both articulators and remodelled it from scratch. Best of both worlds. Even better than that, because once you have a CAD working file, you can modify or iterate effortlessly, much more easily than trying to modify an STL or other mesh file.