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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.

Raspberry Pi case for Prusa i3 / i3 Mk2