Pattern recognition in three dimensional image is highly sensitive to assigned value and formation of voxels (pixels for two dimension case). However, occurred while digital imaging, digitization error leads to unpredictable noises in image data. Skeletonization, a powerful tool of pattern recognition, is sensitively dependent on boundary formation. Without successful controlling of the noises, the results of skeletonization can not be allowed as a stable solution. To minimize the effect of noises affecting to boundary formation, we developed a robust processing method useful in skeletonization technique for pattern recognition. Finally, we provide rigorous test results achieved throughout simulation on analytic three dimensional image.