I have en path created with the Pen tool - my wish is to move each vertex in a 3D space (Z, Y, X axis ) and I can move each vertex around the X and Y axis, but I can not move the vertex of my Z axis - I has enabled the 3-D cube and I use the "Selection tool" to move around the vertex .....
This is not possible at this time in After Effects.
Moving verticies in 3D space requires either a full-fledged 3D software package, or a 3rd-party plugin such as Digieffects Free Form.
Free Form does not use mask verticies, however. It creates it's on vertex structure independent of the inherent masking tools in AE.
A sneaky little trick to paint 3D paths would be to use Trapcode Particular's Path mode based on a 3D light's motion.... The keyframes of the light woult then act as the vertices. Short of that consider other tools. As Steve mentioned, Freeform is a good place to start but there are tons of others as well (3D Stroke, Form, Boris Continuum, Zaxwerkes Serpentine etc.) Just look here for more detailed info. Even some effects that come with AE can be tweaked to look 3D-ish like CC Ball Action's Twist for instance. If you know how to create maps for it, even Card Dance could be used to draw some sort of 3D path. For simple things, you can always map stuff on CC Cylinder and CC Sphere, of course. Quite a few possibilities even without a real 3D program.