With the latest 3DS Update, you can keep your 3DS organized.
Here’s how it works.

Make your 3DS Menu smaller, using the 4 squares, at the top of your 3DS’s Bottom Screen.
This will make the ‘drag and drop’ process a lot easier.

Get to an empty slot.
And tap on the “Create Folder” button, at the bottom.

Change the name.
This is to make it look more organized.

Now just drag and drop the icons you want to have in that Folder.
Check it out, and it looks nice, don’t you think?