When extruding a raster layer (or the raster representation of a Smart Object), Photoshop traces a vector path around the layer then generates an extrusion of that path. The tolerance for the tracing can be set in the dialog for the Make Work Path command that converts a selection to a path, but in the case of a geometric shape such as a hexagon, much neater results will be produced from a path that's directly created with vector tools. The Polygon Tool in Shape mode or Path mode can create a good hexagon for extruding.

Here's a screenshot with an extruded hexagonal Shape layer on the left and an extruded hexagonal raster layer on the right.

A Vector Smart Object layer will not help. The raster representation of the VSO will be extruded with the distorted result seen above.

When you've got an extrusion that you like, I'll tell you how to work around the rotation problem.

There's a problem with rotating an individual object (mesh or extrusion) that's inside Scene. See thread CS6 timeline bug when rotating a sphere

In the thread, I give a clunky solution for rotating an individual object through 360 deg by keyframing at 0, 120, 240 and 360. You won't need to do that, though.

Fortunately, the entire Scene can be rotated without problem. You have only one extrusion object inside Scene, so rotate the whole Scene instead of the object: keyframe Scene rotation at 0 deg followed by a keyframe of 360 deg will rotate correctly.

If you're making a looping animation then you'll want the final frame to be just before 360 deg. The rotation will be happening over n frames, so make the rotation value in the final frame be (360 -  (360 / n)) deg.

I tried to post the following before you edited your post, so here it is anyway, in case it is useful to anyone.

The tree in 3D panel misleadingly suggests that the lights and camera are inside Scene. That's not the real situation. The lights and camera are really outside of Scene. So the rotating Scene will be lit the same as if only the extrusion object was rotating.

n is the number of frames. If the animation is 5 seconds at 30 fps then there'll be 150 frames.

n = 150

(360 - (360 / n))  =>  (360 - 2.4)  =>  357.6

The coordinates of an individual object (your extrusion for example) inside Scene are relative to the Scene coordinates, so the extrusion should have been created with X,Y,Z = 0,0,0. Maybe you moved the extrusion object at some time, so set its coords to 0,0,0 in Properties panel.

SFS-DPS wrote:

 

Not sure why my object in not centered..however to solve i put my camera at top view and drew some guides. then manually centered the polygon. It seems centered when my z axis is at -209 all other ordinates are at 0.

The object's coords are relative to Scene and Scene's own coords are in a world space, so maybe you moved Scene (which includes the object) earlier and now a move of just the object by 209 restores the object to its original location in the world while Scene remains moved in the world.