We theoretically study a particular plasmonic structure with stereo nanoholes array in metallic film, which has remarkable abilities to manipulate the optical polarizations at optical frequencies. The main property is that any linear polarization states including a complete 90° optical rotation can be obtained in transmission by proper structural design in combination of enhanced transmission efficiency. Together with the polarization change, surface plasmon propagation bounded on the surface of transmission side also can be modulated. Furthermore, an analytical Coupled Mode Method (CMM) is developed by introducing a frequency dependent coupling coefficient to describe such optical rotation property in stereo plasmonic systems.