The present disclosure describes a method that includes forming a dielectric layer over a contact region on a substrate; etching the dielectric layer to form a contact opening to expose the contact region; and pre-cleaning the exposed contact region to remove a residual material formed by the etching. During the pre-cleaning, the first contact region is exposed to an inductively coupled radio frequency (RF) plasma. Also, during the pre-cleaning, a direct current power supply unit (DC PSU) provides a bias voltage to the substrate and a magnetic field is applied to the inductively coupled RF plasma to collimate ions.