This is a pretty good reference I used to implement cross-eye stereo (I've moved to the Jogl API, but it should be possible in Java3D -- put a TransformGroup at the root of your scene and translate by the eye-separation and update the viewpoint direction):
You don't need to go the long-winded way using two transforms. The Canvas3D supports a two eyed view directly (Canvas3D.setMonoscopicViewPolicy(Canvas3D.FIELD_RIGHT/.FIELD_LEFT)).
Michael
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