The Iris based identification systems have been noticed exceedingly, presently. In this process, the iris should be segmented from captured eye image. The low contrast between pupil and iris, usually, will harden the segmenting process and will decrease the accuracy of detecting boundary between them. In order to segment the iris more precise, the authors propose a new technique using a difference function and a factor matrix. They also modify the segmentation operator to detect the pupil and iris as ellipse instead of circle. Experiments show that the proposed technique can segment the iris region and pupil region precisely. Based on their result, 99.34% of eyes have been segmented accurately in 1.24s averagely.