An apparatus and methods for scanning and measuring transparent fibers. One example method includes placing the transparent fibers on a platen of a flat-bed style scanner and compressing the transparent fibers to the platen with a cover including a non-reflective surface adjacent to the transparent fibers. The method also includes spacing an image sensor apart from a light source on a carriage below the platen and transmitting light from the light source through the platen. The light refracts within the transparent fibers and reflects from the transparent fibers to the image sensor and is absorbed by the non-reflective surface of the cover. The method also includes capturing an image of the transparent fibers with the image sensor.