first of all thanksAre you projecting on a 3D object you printed ? In this case just calibrating should be enough, modifying the mesh wouldn't be a good idea.
If the real-world 3D object doesn't exactly match the OBJ, you can use the "Edit Mesh" option in MM or modify the mesh in your 3D modeler (with more flexibility and working in 3D space, but more complex).
To move an invisible vertex in MM, there's a tweak, move the complete edge to a place where both extremities are visible, move back the point you didn't want to move, then you can move the one that was not visible.
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