You can hide big obstacles by using the X-Ray mode. After you use it, you can pick up the needed item.
Just tap the yellow icon with an arrow:

Then tap the icon with a Tree to activate the tree special mode:

 

The biggest obstacles will be hidden and you will see the needed item. In this mode, you can also place your buildings in a more efficient way.

To return to the normal view, tap the icon with a Tree.