Christian Aurich developed a script to import Eagle boards into FreeCAD. This way he is able to design custom enclosures.
The common solution until now is to export your board with eagleUp and assemble it with a case in Sketchup. This also gives you some drawbacks. The most important to me was that the Sketchup files are mesh based like the data used for 3D printing usually, but for further use in CAD systems this is not really usable. You also will not be able to get a STEP model that you can give to your costumers out of this data.
Script lets you import Eagle boards for use in FreeCAD - [Link]