One method disclosed herein includes performing a plurality of conformal deposition processes to form first, second and third layers of material within a contact opening, wherein the first layer comprises a contact insulating material, the second layer comprises a metal-containing material and the third layer comprises a conductive cap material, wherein the third layer is positioned above the second layer. The method further includes forming a contact ion implant region that is positioned at least partially in at least one of the first, second or third layers of material, forming a conductive material above the third layer and removing portions of the layers of material positioned outside of the contact opening.