I've started 3D printing monsters to replace the standees that the game came with. I always print my minis without bases (to make supports easier), so I figured that it would be nice to have the monster's numbers as part of to the base. That left me needing a way to denote Elite vs. Non-Elite, so I made a separate piece that can be painted yellow (or printed in yellow, if you've got that filament around), then snapped onto the underside of the main base. There's a 1 mm tall and a 2 mm tall version of that base, depending on how much visibility you want/need for the elite marker (my photos are all of the 1 mm elite base, but I think that I'm starting to prefer the 2 mm version).
I've included the Blender file, to make it easier to change in case anyone wants to customize it (or replace my plain base with something more ornate or whatever.
Big thanks to Isaac Childres for publishing the Creators Kit, which allowed me to use the actual Gloomhaven font for the numbers on the bases =) I made the numbers outstanding rather than inset in order to make them easier to paint (I just used a sharpie to blacken mine).
Update: I've printed a lot of these as I've been making more and more monster minis. I've found that .1 mm layer heights seem to work really well and that they're quite difficult to print (they're so thin that they like to warp and get caught on the printer head). I've printed my last 3 batches with a 3 mm brim, which is a pain to clean up, but I haven't run into warping issues ruining my prints since I started using the brim.
Also, use a cool infill pattern to make the top layers look nice. I'm personally fond of Slic3r's Archimedean Chords pattern.
Note: the Skeleton in the photo is my Gloomhaven Living Bones model, available at https://www.thingiverse.com/thing:3024751
I wrote a blog post about how I made these at https://objectforge.blogspot.com/2018/10/new-thing-numbered-bases-for-gloomhaven.html