A method of pattern data preparation includes the following steps. A desired pattern to be formed on a surface of a layer is inputted. A first set of beam shots are determined, and a first calculated pattern on the surface is calculated from the first set of beam shots. The first calculated pattern is rotated, so that a boundary of the desired pattern corresponding to a non-smooth boundary of the first calculated pattern is parallel to a boundary constituted by beam shots. A second set of beam shots are determined to revise the non-smooth boundary of the first calculated pattern, thereby calculating a second calculated pattern being close to the desired pattern on the surface. The present invention also provides a method of forming a pattern in a layer.