AFAIK there is no way to backup saved games on a 3DS without modding one. I know a negative answer is not that helpful, but it is what it is.
If you have access to a second 3DS, you can do a system transfer from your device to that one (this should include your saved games), make a backup of the SD card of that second system, then transfer back. In case your 3DS breaks down, it should be possible to redo the transfer by contacting Nintendo customer support, then restore your games from the backup on that second system. Considering that you're limited to 1 system transfer per week, and the fact that you need a second device (which will be wiped) to do it, I doubt this is a useful approach unless you own two devices.