We need to flatten the brain cortex to smooth surface, sphere, or 2D plane in order to view the buried sulci. The rendered 3D surface of the segmented white matter and gray matter does not have the topology of a sphere due to the partial volume effect and segmentation error. A surface without correct topology may lead to incorrect interpretation of local structural relationships and prevent cortical unfolding. Although some algorithms try to correct topology, they require heavy computation and fail to follow the deep and narrow sulci. This paper proposes a method that corrects topology of the rendered surface fast, accurately, and automatically. The proposed method removes fractions beside the main surface, fills cavities in the inside of the main surface, and removes handles in the surface. The proposed method to remove handles has three-step approach. Step 1 performs smoothing operation on the rendered surface. In Step 2, vertices of sphere are gradually deformed to the smoothed surfaces and finally to the boundary of the segmented white matter and gray matter. The Step 2 uses multi-resolutional approach to prevent the deep sulci from geometrical intersection. In Step 3, 3D binary image is constructed from the deformed sphere of Step 2 and 3D surface is regenerated from the 3D binary image to remove intersection that may happen. The experimental results show that the topology is corrected while principle sulci and gyri are preserved and the computation amount is acceptable.