Yes It is easiest to separate the smallest tree firs then the next smallest and what is left is a fairly undisturbed bigger tree.

Steve

Okay, thank you! I think I'll try taking out the baby one and see how everyone does. :)

Are you sure it is 3 separate trees? Many Meyer lemons grow in a bush form rather a single stock tree.. You better how before you treat your tree.

I was thinking the same thing as Silica. You can keep it as it is by pruning out the middle smaller branches so they don't cross or rub.

Personally..... if it's growing great then leave it alone; "... if it ain't broke don't try to fix it."

Looks cutting-grown. But it's too hard to tell what is what without totally removing all the soil. And that will likely spin it into shock. I wouldn't do anything now. It's not going to recover from the shock as readily as in spring/early summer.

If you want another plant, take cuttings next summer, or buy another one. If you want a single trunk, just clip off the others at ground level. I'd just leave it alone personally.