The original design of the Navio 2 case by @mcancion is great but didn't leave enough space to get the SD card out on the Raspberry Pi 3 (which has no spring mechanism) and the GPS connector on the top needed more room. Also I thought my older Navio+ could benefit from the same design, so remixed another top for that.
All Navio models can share the same base, so long as they are used with a Raspberry Pi 2 and 3. The extra space for the SD slot on Raspberry Pi 2 is not a problem, in fact better there too to get your finger in to eject. So it's really quite universal now.
If you like this please also like the original piece to give kudos to the creator (http://www.thingiverse.com/thing:1659565). @mcancino is aware of the issues and said he will update the original sometime in the future.
The Tinkercad files are available here in case you wish to review the changes or adjust them further:
Navio 2 Top: https://tinkercad.com/things/cvdVhOuZqBk
Navio Plus Top: https://tinkercad.com/things/4z31DjB6Dxi
Navio Base: https://tinkercad.com/things/3KqMfuJ8s5K