An apparatus and method for processing a substrate using neutralized beams are provided. A substrate processing apparatus includes an ion source generating device configured to form an ion source. An ion extraction device is configured to extract and accelerate ions from the ion source. An ion neutralizing device is configured to convert the ions extracted and accelerated from the ion extraction device into neutralized beams. A remaining portion of the ions extracted and accelerated from the ion extraction device is not converted into the neutralized beams. A substrate support is configured to support a substrate such that the neutralized beams are directed towards the substrate support. A substrate power supply is configured to apply a voltage to the substrate support such that the remaining portion of the ions that is not converted into the neutralized beams is directed away from the substrate support by the applied voltage of the substrate.