A method of aligning a tool, the method comprising: capturing a first magnified image of a plurality of microscopic native features (204, 206) belonging to an inherent microscopically visible texture in a first region of a moving workpiece using a first imaging unit of an imaging system at a first location; capturing a second magnified image (300, 400, 500, 600, 700, 800, 900) of the plurality of microscopic native features (304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) in the same first region of the moving workpiece using a second imaging unit of the imaging system at a second location, a time interval passing between capturing the first magnified image and capturing the second magnified image (300, 400, 500, 600, 700, 800, 900); determining a correspondence between the plurality of microscopic native features (204, 206) of the inherent microscopically visible texture of the workpiece as captured in the first image and the plurality of microscopic native features (304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) of the inherent microscopically visible texture of the workpiece as captured in the second image (300, 400, 500, 600, 700, 800, 900); determining a positioning information of the moving workpiece relative to the respective first and second locations (112, 116), using a controller to analyze the microscopic native features (204, 206, 304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) having the correspondence between the first and second images (200, 300, 400, 500, 600, 700, 800, 900); and aligning the workpiece and the tool, based upon the positioning information. capturing a first magnified image of a plurality of microscopic native features (204, 206) belonging to an inherent microscopically visible texture in a first region of a moving workpiece using a first imaging unit of an imaging system at a first location; capturing a second magnified image (300, 400, 500, 600, 700, 800, 900) of the plurality of microscopic native features (304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) in the same first region of the moving workpiece using a second imaging unit of the imaging system at a second location, a time interval passing between capturing the first magnified image and capturing the second magnified image (300, 400, 500, 600, 700, 800, 900); determining a correspondence between the plurality of microscopic native features (204, 206) of the inherent microscopically visible texture of the workpiece as captured in the first image and the plurality of microscopic native features (304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) of the inherent microscopically visible texture of the workpiece as captured in the second image (300, 400, 500, 600, 700, 800, 900); determining a positioning information of the moving workpiece relative to the respective first and second locations (112, 116), using a controller to analyze the microscopic native features (204, 206, 304, 306, 404, 406, 504, 506, 604, 606, 704, 706, 804, 806, 904, 906) having the correspondence between the first and second images (200, 300, 400, 500, 600, 700, 800, 900); and aligning the workpiece and the tool, based upon the positioning information.