Once you enable the 3D option, the 3D Scale tool is available. You will see one of two things:
A scaling rectangle appears if your drawing is flat.
A scaling cube appears if your object has some rotated layers around the pivot points, indicating the different axes. If you click and drag on this scaling cube, it will scale proportionally on all axes.
Click on one of the three control points to scale the shape on one axis. Hold down the Shift key to scale the object proportionally. When the control point is selected, it turns pink.