You can do what I did:
1. Backup your SD Card.
2. (Optional) Backup/Dump any games you wanna save as a .CIA archive using GodMode9.
3. Delete all of the contents on your SD Card.
4. Power on the 3DS, booting into CTRNAND.
5. (Optional) Go to System Settings > Data Management to delete any DSiWare installed to NAND, if you wanna recreate a full format.
6. Put the SD Card into your 3DS, to let it create Home Menu data/a new Nintendo 3DS folder.
7. Follow 3ds.guide, following the Homebrew Launcher/Finalizing Setup pages only, as you do not need safehax/SafeB9SInstaller as it's already installed.
And you'll have a 3DS that acts as if it's been formatted.
Now that isn't a full system format, but that should be enough for most people.
Sent from my SM-G360T using Tapatalk