To activate mods, you will have to activate game patching in the Luma 3DS config. With default settings you can do this by holding SELECT button while booting your New 3DS. Normally the Luma 3DS config will pop up. Use the D-Pad to navigate to: Enable Game Patching
Then Press A to activate it and START to reboot console after proceeding. I'm Sorry that i forgot to tell.
Here is a basic explanation on how to patch your Minecraft: New Nintendo 3DS edition game.
-Luma 3DS CFW
-A Digital or Physical copy of Minecraft: New Nintendo 3DS edition
-A SD card from your 3DS containing Luma 3DS (and Minecraft if you purchased digital)
-A device that you can use to download Mods and install them on SD card. (PC is recommended)
Navigate to your SD card using your PC, Tablet etc. to the following location:
If you already used Mods on 3DS, there will be a folder called "titles", if not, create one. Once you have it, create a folder that's Name Matches your Game's Title ID.
For European Game copy it will be "000400000017CA00"
For USA Game: "00040000001B8700"
Now, once you've downloaded a mod, put the content into this location:
You are now almost done for Preparation. But certain Users won't include the correct location Template in their Upload. But i will include 2 folders, one for EUR, one for USA, so you can unzip the file, navigate to correct Region folder, then continue to Title ID folder. It will contain a "romfs" folder that contains the correct Location for mods, so you can just drag and drop
/romfs into your regions Title ID folder. Every mod will have /romfs, the important thing are the included subfolders. If a folder is already on your SD card, just enter this one and create the missing folders to put content inside.