Have the three items you want to merge next to each other and then move one of the items on to the other by clicking your mouse while the pointer is on the item and then hold down your mouse button to move it on to one of the other two identical items you wish to merge.. The third item automatically merges with it. Again the items you want to merge must be next to each other. They don't have to be in a straight line, but they do have to be touching each other. If the items aren't next to each other, you can move the items so they are next to each other by using your mouse and holding the mouse button down and dragging the item where you want them..
OR
If you have two items next to each other, you can pick up (using you mouse and holding down the button) the third item anywhere on the farm and plop it on top of one of the two identical items that are next to each other and they will merge autmatically. You can do it either way.
I put all of my identical items next to each other so the farm doesn't become a complete mess. Then I merge them. That way I know what items I have for merging.