Embodiments of the disclosure provide methods and system for manufacturing film layers with minimum lithographic overlay errors on a semiconductor substrate. In one embodiment, a method for forming a film layer on a substrate includes supplying a deposition gas mixture including a silicon containing gas and a reacting gas onto a substrate disposed on a substrate support in a processing chamber, forming a plasma in the presence of the depositing gas mixture in the processing chamber, applying current to a plasma profile modulator disposed in the processing chamber while supplying the depositing gas mixture into the processing chamber, and rotating the substrate while depositing a film layer on the substrate.