I'm not sure you can actually get it anymore.
If you can, then that's fine. I'll tell you how to get it.

First: Set up the email used on your 3Ds to ClubNintendo.
(Make a profile on ClubNintendo using your 3Ds email)

Second: There should be a list of tabs somewhere on your new profile page that's lined side by side across the page.
(Sorry. Can't remember which one you click on. Pretty sure it's on the right side though)

Third: The tab that you should have clicked on should be kinda like a "To-Do" tab, with a list of things you should do. One of those options should be Flipnote 3D. Click on that.

Fourth: It will ask you a bunch of questions. Answer them truthfully. It's trying to find where/which Ds you're trying to link in.

Finally: Just go to the Nintendo Eshop when it's done, and type in the code that it gives to you.
(When Club Nintendo finishes finding your Ds, it will produce a code)
Put this code into the Eshop, and congradulations. Flipnote 3D is yours :D