In one embodiment, a wafer alignment system, comprises a radiation source to generate radiation, a radiation directing assembly to direct at least a portion of the radiation onto a surface of a wafer, the radiation having a polarization state, an optical analyzer to collect at least a portion of the radiation reflected from the wafer, the wafer including at least a first region having a first grating pattern oriented in a first direction and at least a second region having a second grating pattern oriented in a second direction, different from the first direction.