Methods for selectively depositing different materials at different locations on a substrate are provided. A selective deposition process may form different materials on different surfaces, e.g., different portions of the substrate, depending on the material properties of the underlying layer being deposited on. Ion implantation processes may be used to modify materials disposed on the substrate. The ions modify surface properties of the substrate to enable the subsequent selective deposition process. A substrate having a mask disposed thereon may be subjected to an on implantation process to modify the mask and surfaces of the substrate exposed by the mask. The mask may be removed which results in a substrate having regions of implanted and non-implanted materials. A subsequent deposition process may be performed to selectively deposit on either the implanted or non-implanted regions of the substrate.