3DS rom extractions

[Swordsmage]

What is the preferred way to extract the ROM for Super Mystery Dungeon? I've previously ripped it through Godmode but I always get an error about missing paths when it comes to building the ROM. So I'm wondering if I need to extract it a certain way like I did for a recent model ripping tutorial I was following for Ultra Sun. Does it need to be decrypted just extracted? Left as a .3DS or a .cia? Thanks in advance. 

[evandixon]

Be sure to decrypt the ROM in GodMode9 first.

[Swordsmage]

That's what I did, I even update Sky Editor whenever one is available, and I'm still getting the "path not found" error when building. Could there be something else I'm doing wrong?