These are holders for the round ship modifiers and other tokens for the Star Trek Fleet Captains board game. The depths of the holders are designed to work with a combination of the base game plus the Dominion expansion, which is what we have. You can also use it for just the base game. It is easy to edit the OpenSCAD file to change holder depth to match your needs.
This should make playing a lot smoother than with digging through little baggies.
There are two versions of the holders: a filament-saving version that just has narrow walls, and a solid version that looks better (and you can print it with 15% infill). In the photo, the round markers are in a solid version while the others are in the filament-saving version.
Update: Dec. 17, 2017: Added a cover for the other holder.
Update: Nov. 24, 2017: Added a lid for the round piece holder.