Abstract: A method and apparatus for controlling ion beam scanning in an ion implanter is disclosed. Before an implant process is commenced, a scan waveform to create a uniform distribution along a magnetic scan axis is determined, using a travelling Faraday detector (24). Charge data from the travelling Faraday (24) is collected into a small, finite number of channels and this is used to create a histogram of collected charge vs. beam crossing time. This is in turn used to correct a target scan velocity to compensate for any dose non-uniformity. The target scan velocity is used as a first input to a fast feedback loop. A second input is obtained by digitizing the output of an inductive pickup in the magnet of the magnetic scanner in the ion implanter. Each input is separately integrated and Fast Fourier Transformed Error coefficients Ferror are obtained by dividing Fourier coefficients from the target scan velocity by Fourier coefficients from the inductive pickup signal.