A pill manipulating system for filling a packaging with pills is provided, aswell as acorresponding method. The system comprises a vacuum pump, a pill manipulatorincluding a hose connected to the vacuum pump, and at least one prong. Theprong(s)has/have an opening at one end sized to retain a pill when the pillmanipulator is in a retainconfiguration and suction is applied, and to release the pill when the pillmanipulator is ina release configuration and suction is reduced. The system includes a vacuumpumpcontrolling assembly including a variable frequency drive, for adjusting anair flow of thevacuum pump based on a selected input, which is representative of a size ofthe pills beingmanipulated, thereby reducing the likelihood of having the at least one prongretainingmore than one pill at a time.