Prerequisites
Your console needs to have custom firmware (CFW) installed. If you do not have it, please go to https://3ds.hacks.guide/ and follow the guide for installing it there.
Make sure the latest version of GodMode9 is installed, it can be downloaded here: https://github.com/d0k3/GodMode9/releases/tag/v2.1.1
To open it, make sure the console is powered off, then press the Start button to load the Luma Chain Loader menu. Select GodMode9 to launch it.
If you want to dump your cartridge, make sure it is inside of the system.
Extracting
Extracting the base game (1.0) is not necessary, but you should just in case. It's RomFS is not referenced much when modding, but if you want to do things like make custom music, for example, then you will have to extract it.
You will need to extract the game's update (1.9) to do anything for modding, as most things will apply to the update.
Extracting the 1.0 RomFS (cartridge)
Open GodMode9
Navigate to [C:] GAMECART
Press (A) on [TitleID].trim.3ds
Press (A) on "NCSD image options..."
Press (A) on "Mount image to drive" and press (A) to enter path
Press (R) and (A) on the "romfs" folder
Press (A) on "Copy to /gm9/out"
Extracting the 1.0 RomFS (installed title)
Open GodMode9
Navigate to [A:] SYSNAND SD
Press (R) and (A)
Press (A) on "Open title manager"
Find and press (A) on "[TitleID] Minecraft: New Nintendo 3DS Edition (KTR-P-BD3E)"
Press (A) on "Open title folder"
Press (A) on the .tmd
Press (A) on "TMD file options..."
Press (A) on "Mount CXI/NDS to drive" and press (A) for yes
Press (R) and (A) on the "romfs" folder
Press (A) on "Copy to /gm9/out"
Extracting the 1.9 RomFS (installed title)
Open GodMode9
Navigate to [A:] SYSNAND SD
Press (R) and (A)
Press (A) on "Open title manager"
Find and press (A) on "000400E[TitleID] Minecraft: New Nintendo 3DS Edition (KTR-P-BD3E)"
Press (A) on "Open title folder"
Press (A) on the .tmd
Press (A) on "TMD file options..."
Press (A) on "Mount CXI/NDS to drive" and press (A) to enter path
Press (R) and (A) on the "romfs" folder
Press (A) on "Copy to /gm9/out"