To bubble items from your Realm, you first need to fill all empty spaces you have left. It is a good idea to fill your extra spaces up with easy to obtain low level items that you can later use, sell, or merge back out of your way when you are finished.

When you fill every space, the game will force you to have two empty squares left. These are what we will now need to fill using the trick in the next step.

It is not easy to fill the last two squares in your Realm, as the game wants these left open (who knows why), but there is a way to do it using Flying Seeds!

You cannot just simply tap a flying seed to fill these last two spaces though.. You must grab one using your cursor and drag it over the edge of one of those last spaces. Once you have it over the space, very quickly let go then immediately tap it again, and as long as it was close enough to the square, it will fill it!
(Note: this trick used to work with other bubbles too, but now only does with the Flying Seeds)

You'll just have to imagine my cursor holding the flower over the square in the first image :)

That's right, after you fill one or both of the last two squares, all you have to do now is move something over the item you wish to put in a bubble.

Since the game wants two squares open... when you try to move an item over another one without having any spaces available, you will replace the lower item with the one you were holding, and the lower item (the one that was still sitting on the ground) will bubble up!

(In this demonstration I was holding the Seed to bubble the Divine Tree - Bubbling will only occur after you let go of the held item)

Once you have moved anything you want out of your way (that is worth keeping) into Bubbles, all you have to do now is use, sell, delete, or mass merge those space-filler items that we didn't care about, and you will now have a more clean and organised Realm to work with.