Not just villains. This would be a great thing for any covert agency as it would allow them to fabricate in-house many things that they would otherwise be unable to covertly buy or manufacture using traditional means. Also, check this out:http://www.eads.com/eads/int/en/news/press.8d764849-d439-475b-93b3-3cc9a7d2ba20.70472f39-dd6f-4428-a792-91d82cb9791b.html
So, if an agency wants a helicopter, they have some options. They can buy a helicopter, and then everyone ever knows they have a helicopter. They can buy the parts for a helicopter, and then anyone who does a little digging knows they have or will soon have a helicopter. They can buy a factory and the materials necessary to build a helicopter, but everyone will know they have a factory (a tremendously expensive factory at that) and can drop by to see the helicopter being made. Or, they can buy a large 3d printer and polymer/ceramic printer stock and then anyone who does some digging will know they have a large 3d printer. The 3d printed helicopter option relies to some extent on spy thriller super-science, but it still sounds like the best option to me.