Note: This is not Flipnote Studio 3D. This is Flipnote Studio, which was free on the DSi Shop. You can get Flipnote Studio 3D from Nintendo.
To install, you'll need to set up custom firmware on your 2DS/3DS/New 3DS first. The guide at 3ds.guide will always be up to date.
These are in the .CIA (CTR Installable Archive) format for 3DS - plunk on your SD card and install with the FBI app, which will be installed while you follow the guide linked above.
Make sure to pick the correct version for your system region, or it won't work.
Also included are downloads for Nintendo DSi Camera and Sound, which can be used in tandem with Flipnote Studio.