That seems wrong. You didn't copy the object. You reproduced its design. The distinction isn't much in the language, but it is important legally.

You couldn't scan the object and print an exact copy, or use still frames from the movie, but you can certainly create your own object and slicer files from scratch to make a novel object visibly indistinguishable from it, or even make a new instance from the original construction recipe (if one exists). You could also take the original prop and make a new photo of it yourself.

All that activity is instead governed by patents, specifically design patents. It is very unlikely that a film production company would seek out design patents for random prop elements that were seen in the final cut of a movie, unless they are to be used for merchandising purposes. Lucas could certainly create a design patent on Obi-Wan's and Darth Vader's lightsaber props, so the licensee could have a protected monopoly on selling the reproductions as toys. In that case, you couldn't 3D-print your own Vader lightsaber. You could still make your own lightsaber design, and print that, but the design patent prevents you from making one that looks specifically like the one in the patent. With no design patent, you can reproduce from scratch anything you see. Copyright is about rote copying of an embodied artwork. Derivative works must include some piece of the original. That isn't what you did.

Alternately, an image or object can be trademarked, wherein certain visual elements can be claimed as symbolic of your work within a specific domain. That's stronger, but narrower protection. If a lightsaber is a trademark image for something like a computer game production company, you couldn't use similar objects or images to promote your own business relating to computers, software, or scientific equipment. But you could probably use it on a beer label with no problems whatsoever, because that's a different domain. You don't need to register your trademark in order to defend it; you just have to use it in commerce. The major characters, unique props, and distinctive sets are all potential trademarks, particularly if they appear in multiple works within the same domain.

Whomever it was that denied you on copyright grounds should not have done so. There is no way to acquire a license because none is necessary. In any case, copyright violation is a civil matter, and only the owner of a copyright has standing to defend it. There is no requirement for anyone else to do it on their behalf.

(I am not a lawyer. This is not legal advice.)

As for Stage 9, it seems like that C&D would have been based on a claim that the bridge set of ST:tNG is a trademarked element of the franchise, in the domains of entertainment and computer software. Copyright is not the issue. The set design was integral to the show and the games based on it; it appeared in almost every episode. That's one of the ways you knew you were watching Star Trek, in addition to the uniforms and logos. If someone were to use a perfectly replicated model of the bridge to produce a video, there could be legitimate brand confusion by a viewer, who might think that their video was officially sanctioned by the Star Trek trademark owner.

Something like Robot Chicken, which uses licensed toys to make videos that include the elements trademarked in the same domain, walks a fine line, that is likely saved only by the crudeness of the reproduction. It is clear that the sets and actors are toys, and not pretending to be the things they represent.