I liked MortenGuldager's screw bit case design so much that I took to openscad to design one for my micro bits. This isn't fully parametric yet, but a few parameters can be customized (see the scad file). I'll clean up the .scad file soon, but I was excited to share it now. Included in the download is the threads.scad file made by Dan at dkprojects.net. I wouldn't have been able to make this without this great little piece of code. Happy Printing!

Update:

Version 1: As MortenGuldager pointed out, this version likely has way too many holes for micro-bits. It's hard to pull out a single bit if you happen to have chubby fingers like mine. Unless you' have a ton of micro-bits, this version isn't for you.

Version 2: I decreased the number of micro-bit holes and made the holder a few mm shorter. This is probably the better option. The lid is the same for both versions.