Using a beam current of an ion beam, a dose amount to a substrate, and a reference scan speed, a scan number of the substrate is calculated as an integer value in which digits after a decimal point are truncated. If the scan number is smaller than 2, the process is aborted. If the scan number is equal to or larger than 2, it is determined whether the scan number is even or odd. If the scan number is even, the current scan number is set as a practical scan number. If the scan number is odd, an even scan number which is smaller by 1 than the odd scan number is obtained, and the obtained even scan number is set as a practical scan number. A practical scan speed of the substrate is calculated by using the practical scan number, the beam current, and the dose amount.