Are you hoping for something colorful and custom, then? Or trying to replace broken parts? If it's broken parts, Asmodee or whoever manages FFG's sales these days will often replace broken parts for free -- it's worth asking!
If you're looking to customize, hmm... bases are tough. They have to be pretty precise to fit into the ship and cardboard and whatnot (not even FFG gets this right quite often... grr...). However, magnetizing might make it a lot easier (so you don't need precise pieces fitting inside slots etc). Maybe explore Etsy, though my quick google search didn't turn up useful results.
I don't know where to search for 3D printing files for that, and you'd want to make sure you got the 2nd edition ones since I think they're slightly different. At this point I'd ask Reddit, or the FFG Forums.