3D transformations are used to make pseudo-3D. And in this 3D space your layer overlaps others. To change its z-pozition use CAlayer's property
@property CGFloat zPosition;
The layer’s position on the z axis. Animatable. The default value of this property is 0. Changing the value of this property changes the the front-to-back ordering of layers onscreen. This can affect the visibility of layers whose frame rectangles overlap. The value of this property is measured in points.