Checkpoint is a 3DS homebrew application that can backup and restore save files for 3DS cartridges, 3DS eShop titles (including GB and GBC virtual console), and NDS cartridges. This tutorial will walk you through its installation and usage.
In order to use Checkpoint, you will first need access to CFW. A comprehensive guide on how to set it up can be found here. If you do not have what you need, you cannot use Checkpoint.
What you need
A 3DS with CFW