Disclaimer:
Modifying the NAND is inherently risky. A bad NAND flash can permanently brick your console. This guide assumes you have a hardmod (soldered connections) or are using godmode9 with a working bootable state. Do not proceed unless you understand the risks and have a verified full NAND backup already saved to your PC.
For a visual walkthrough on managing system files and installing homebrew on your 3DS, check out this comprehensive guide:
Before attempting any NAND operation, you need specific tools.
Tool Required: GodMode9 (GM9) is the standard tool for this process. Backup Procedure: