Currently, you can create main files (backups of your save data for games) using hax to load up saveDataBackup (for those who don't know, it's homebrew) on most, if not, all 3DS types and firmwares. Using this app, you can create backups and import backups of your save datas. PKHeX is compatible with these and can edit your save data for XY and ORAS. It's often recommended you make a backup, and, as far as I know, there isn't a backup feature for main files. Tampering with the main file in certain ways is always risky, and data corruption or other problems can occur. Plus, some people just like to keep backups in case certain issues arise such as losing pokemon, accidentally releasing them, et cedera.
Could there be a backup feature implemented?
If a future version isn't to come for a while, I have made a temporary solution to Windows users who would like to backup their main files. I made a small two-line batch file which copies the main file from your SD card to a folder of your choice, then opens the folder which it copied to. Already tried it, and it works.