A pill manipulating system for filling a packaging with pills is provided, as well as a corresponding method. The system comprises a vacuum pump, a pill manipulator including a hose connected to the vacuum pump, and at least one prong. The prong(s) has/have an opening at one end sized to retain a pill when the pill manipulator is in a retain configuration and suction is applied, and to release the pill when the pill manipulator is in a release configuration and suction is reduced. The system includes a vacuum pump controlling assembly including a variable frequency drive, for adjusting an air flow of the vacuum pump based on a selected input, which is representative of a size of the pills being manipulated, thereby reducing the likelihood of having the at least one prong retaining more than one pill at a time.