MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I can't answer that as I don't own a Pi 3 but I doubt it. I use Pi 2 so I specifically found and remixed my design from hofftari's Pi 2 case found here. (https://www.thingiverse.com/thing:1325370). Maybe someone else here will have a beter answer for you but I really doubt they are the same shape so doubt my case will work for you.