A method of manufacture of an integrated circuit system includes: fabricating a substrate having an integrated circuit; applying a low-K dielectric layer over the integrated circuit; forming a via and a trench, in the low-K dielectric layer, over the integrated circuit; forming a structure surface by a chemical-mechanical planarization (CMP) process; and applying a direct implant to the structure surface for forming an implant layer and a metal passivation layer including repairing damage, to the low-K dielectric layer, caused by the CMP process.