I used the instructions on this guide to back up my save file.
Basically, you’ll download the zip file from that page, copy the lt-saveout.bin file onto the root of your SD card, put the SD back in your 3DS/ 2DS, start your game with your mayor, let Isabelle load the town to the point where you can move around, go to the internet browser from the home screen, go to the url listed on the guide I linked to, and viola! your backup file is created on your SD card under the name mori.bin. You should store this somewhere safe on your computer and rename it so that you’ll know exactly what it is. If you somehow corrupt your game, you can restore it with this file. Instructions for restoring your save file are also in the linked guide, along with town-edit hacks.
Though I (mischacrossing) have used some of these hacks, I will not promote them because they can mess up your game, and I don’t need that blame on me. They have worked safely for me, but use them at your own risk.. with a save file backed up of course. Read all instructions thoroughly.