Application of the directed self-assembly (DSA) of block copolymer (PS-b-PMMA) to the hole shrink process has gained large attention because of the low cost and the potential for sub-lithographic patterning of contact, via and cut masks (Ref. [1-2] and references therein). In order to realize the DSA hole shrink process for manufacturing, however, one still has to resolve a few critical issues such as morphological defects and placement errors . The morphological defect here indicates the PS residual layer lying between the vertical PMMA cylinder and the substrate, which prevents the PMMA cylinder from touching to the bottom surface. Such underlying defects cannot be observed by conventional approach with the top-down SEM images. In this study, we have utilized a simplified model, so-called the Ohta- Kawasaki (OK) model [4-5] to optimize the DSA hole shrink process. The advantages of the OK model are considerably low computational expense and reasonable accuracy. First, we demonstrated that the OK model could indeed predict complicated, three-dimensional morphologies of the diblock copolymer in the pre-patterned hole. All the results were computed within one minute, and they were reasonably comparable to those obtained from the self-consistent field theory (SCFT) . Then, we calibrated the model parameters with the cross-sectional TEM images, minimizing the errors between the simulated thickness of PS residual layer and the experimental data. The calibrated model was used for the optimization of the guide hole shape and for the exploration of the multi-cylinder case.