3ds Rom Extractor Now

provides extensive documentation on how custom firmware allows users to decrypt and extract data directly from their own hardware.

There are several popular utilities depending on your operating system and technical expertise: 3ds rom extractor

Encrypted repacking is complex. You will usually repack as "decrypted" and rely on your emulator (Citra) or custom firmware (Luma3DS) to run the loose files via LayeredFS (mod directory) rather than repacking into a full ROM. you will see:

Extracting classic ROMs (like NES or Game Boy) from 3DS Virtual Console titles for use on other devices. Top 3DS ROM Extractor Tools 3ds rom extractor

The tool will run ctrtool and 3dstool in the background. You will see green lines of text flashing. When it finishes, you will see: