A semiconductor device and a manufacturing method thereof in which the peripheral length of an aperture and the mechanical strength of cylinders in a cell can be increased without changing the occupation rate of patterns in the cell. By forming a slit in the middle of each mask pattern so as not to expose parts of wafer, the aperture of the wafer becomes nearly cocoon-shaped with a constriction in the middle. Thereby, the peripheral length of the aperture can be increased without changing the occupation rate of the mask patterns in a cell. Further, the shape of the bottom of the aperture also becomes nearly cocoon-shaped with a constriction in the middle, and therefore it is possible to increase the mechanical strength of cylinders.