The graphoepitaxy of symmetric PS-b-PMMA BCP film on the PS 60 mol% brush layer is carried out using the chemically homogeneous topological pattern of SiO2 layer and the home-made solvent annealing tool. It is confirmed by atomic force microscopy that PS-b-PMMA film on the periphery of the trench flows into the trench during the solvent annealing, so that the film thickness in the trench is thicker than that on the un-patterned area. The solvent annealing time dependence indicates the lamellar orientation in the trench changes from a mixture of the lamellar domain parallel and perpendicular to the side walls to the lamellar domain parallel to the side walls, and then changes back to the mixture, although the lamellar orientation perpendicular to the substrate remains the same. This result is also discussed with a free energy model for confined di-block copolymer. The lamellar domain parallel to the side walls indicates that the surface tensions of PS and PMMA blocks absorbing solvent vapor with the PS 60 mol% brush layer are not the same during the solvent annealing at 55 °C. Furthermore, the free energy difference between the parallel and perpendicular orientations is supposed to fluctuate due to the dynamics of PS-b-PMMA molecules by the solvent annealing, so that the lamellar orientation results in either of the lamellar domain parallel, perpendicular, or the mixture.