Follow the on-screen prompts to "clean up" the SD card and install the system apps to your Home Menu.
Only download pre-made zips from trusted community members on GBAtemp or official guide sites. Malicious files can brick your console.
Always back up your sysNAND via GodMode9 before running automated scripts from a zip file.
Are you trying to for a specific custom firmware version, or are you having trouble running a script from a file you already downloaded?
Copy all files and folders (e.g., 3ds , cias , luma , gm9 ) directly to the root of your 3DS SD card. Finalize on Console:
Ensure you have the latest boot.firm and boot.3dsx from the Luma3DS GitHub . These should sit at the root of your SD card (and thus the root of your zip).
Insert the SD card and hold while powering on to enter GodMode9 .
For the most up-to-date and safest methods, the community-standard resource remains the 3DS Hacks Guide .