A laser polarization control apparatus includes a polarization modifying device, such as a liquid crystal variable retarder, and a controller. The polarization modifying device receives a laser beam and modifies the polarization of the laser beam. The controller, which is connected to the polarization modifying device, adjusts an input to the polarization modifying device in order to control modification of the polarization of the laser beam based on alignment of a structure to be processed by the laser beam. For example, the polarization of the laser beam may be rotated to correspond with the alignment of a link in a semiconductor device to be cut by the laser beam. The polarization modifying device is configured for incorporation into a laser processing system that produces the laser beam received by the polarization modifying device and that focuses the laser beam modified by the polarization modifying device onto a workpiece that includes the structure to be processed by the laser beam. An analyzer tool receives the laser beam modified by the polarization modification device and measures the modification of the polarization of the laser beam by the polarization modification device.