From the home menu, tap on the software with the save data, slide the triangle icon from the bottom left corner and select save-data backup. Backup can also be done when deleting downloaded software by selecting data management from the home menu, click Nintendo 3DS then software, select the software to be deleted and click create save-data backup and delete software.
The save-data feature allows backup of Nintendo 3DS software and most virtual console games. For system requirements or to update a system, visit the Nintendo website. Up to 30 backups can be created which are saved on the SD card.