now i am able to get the intersection point …
used your code and tweaked according to my requirement…
Point3f center = new Point3f();
Vector3f d = new Vector3f();
canvas.createPickRay(mouseClickPos_X,mouseClickPos_Y, center, d);
PickResult r = new PickResult((Shape3D) selectedNode, 0);
QuadIntersection t = new QuadIntersection();
Geometry geo = r.getGeom();
r.transform(center);
r.transform(d);
Vector3f pos1 = new Vector3f();
Vector3f pos2 = new Vector3f();
Vector3f pos3 = new Vector3f();
Vector3f pos4 = new Vector3f();
geo.getVertex(0, pos1);
geo.getVertex(1, pos2);
geo.getVertex(2, pos3);
geo.getVertex(3, pos4);
t.set(pos1, pos2, pos3, pos4);
float closestIntersect = Float.POSITIVE_INFINITY;
float f = t.test(center, d, closestIntersect);
now i am getting correct X,Y,Z values , even on Translation and Rotation about Z axis ,on clinking on vertices i am getting thier correct values…but when i apply rotation about X and Y axis corresponding x and y values are coming wrong…
In my project getting exact co-ordinates is very important …one more thing…if one of the cube face is at an angle to my view direction and on click of that face i need to change my view to be normal to that face…that is that face is facing the view direction …how to go about it…
thanks for the help … 
P.S : i am using PARALLEL_PROJECTION