We don’t currently have a 3D scanner, but there are a couple of options that might be helpful to you and your students.
With the Lego Digital Designer (http://ldd.lego.com/en-us/) you can build Lego models on the computer. (Then you can export parts lists and go buy the bits you need.)
But there’s also a path you can take to get the models out of Digital Designer and into a format that can be 3D printed.
There are a variety of ways to do this—but here’s an (slightly over-complicated) example:
This software is in the video, but also pretty good and actively developed:
I’d be happy to draft up a few instructions to help with this process—I’m sure there are others grappling with the same sorts of questions.