A system and method for creating a beam current profile that eliminates variations that are not position dependent is disclosed. The system includes two Faraday sensors; one which is moved across the ion beam and a second that remains at or near a certain location. The reference Faraday sensor is used to measure temporal variations in the beam current, while the movable Faraday sensor measures both the position dependent variations and the temporal variations. By combining these measurements, the actual position dependent variations of the scanned ion beam can be determined. This resultant beam current profile can then be used to control the scan speed of the electrostatic or magnetic scanner.