Hey there,
This is an interesting project. As far as I understand. You have scanned data, from which you need to extract a printable area.
If that Is the case this is how I see the things, and some questions that emerge:
1) Will this be a stand alone application, or maybe a script for an application with already build tools like Zbrsuh?
2) The area that we will make printable should be user input, will it be resizable?
3) After importing the STL file, and choosing an area for print, a mesh smoothing should be applied.
4) The output should be again STL file.
My name is Valkan Pavlov. I have good experience in working with printable meshes, but unlike many others I have an experience in scripting, and some of mian programming languages. I understand, and have the tools to provide what you search for.