A method of manufacturing a semiconductor device is provided as follows. A mask layout for forming a target pattern of a multi-height cell including a rectangular notch is generated. A preliminary rectangular mask pattern corresponding to the rectangular notch is detected from the mask layout. The multi-height cell is formed of standard cells arranged and connected to each other in a direction and the rectangular notch is disposed between two adjacent standard cells. A hexagonal mask pattern is, in response to the detecting of the preliminary rectangular mask pattern, placed on at least one short side of the preliminary rectangular mask pattern to generate a combined mask pattern. An outer boundary of the combined mask pattern remains in the mask layout and corresponds to the rectangular notch of the target pattern. A target mask and the semiconductor device are formed based on the combined mask pattern.