You are able to create selections from all of your plant layers.

The Selections tab menu.

There is a check box for each of the following layers: Trunk, Branch, Leaf and Custom Object.

Clicking in the check box will create a selection tag, in the Objects Manager, for the applicable item.

Leaf selection tag highlighted in the Objects Manager.

Clicking on the appropriate selection tag (see Leaf in the image shown above) will enable you to assign layers, such as materials, to this item, individually.

This is demonstrated in the image below, where the material (Mat) has been selected and the Leaf tag has been dragged into the Selection link field.

Mat material highlighted and the Leaf tag visible in the Selection link field.

You can also use the selections to restrict Cinema 4D built-in deformers, using a restriction tag.

Displacement.mp4

Animation to demonstrate displacement of the Custom Object layer alone, using the selection tag as deformer restriction.