This is a simple C rewrite of Python 3DSFAT16tool by Cearp and Swarzesherz. You may use this to dump and decrypt / inject and encrypt the FAT16 partition from your 3DS console NAND backup.
Usage instructions are found on: http://gbatemp.net/threads/port-release-3dsfat16tool-c-rewrite-by-d0k3.390942/
The FAT16 image can be viewed and edited via WinImage or OSFmount (the better alternative) on Windows. On other OSes just changing the extension to .ISO and mounting it may be enough.