The directed self-assembly of polymer-polymer-solvent ternary blends on heterogeneously functionalized substrate is investigated with a three dimensional numerical model. The numerical simulation results are quantitatively verified by the experimental results. The phase separation of PS-PMMA-DMF blends are spin coated on a substrate functionalized by ODT/NH2 on Au surface. While many simulation parameters are set to the experimental conditions, other unmeasurable material constitutive model parameters are estimated from the real experiment observations. The effects of the spin speed, pattern periodicity, PS/PAA composition ratio, and the PAA molecular weight are investigated in both the experiments and numerical simulation. The simulation results are verified by comparison to the experimental results. During the verification process, numerical optimization methods are employed to determine the unmeasurable physical parameters. Quantitative methods are introduced for assessment of the results. (C) 2011 Elsevier Ltd. All rights reserved.