This invention concerns a method and system for single ion doping and machining by detecting the impact, penetration and stopping of single ions in a substrate. Such detection is essential for the successful implantation of a counted number of ³¹P ions into a semi-conductor substrate for construction of a Kane quantum computer. The invention particularly concerns the application of a potential across two electrodes on the surface of the substrate to create a field to separate and sweep out electron-hole pairs formed within the substrate. A detector is then used to detecting transient current in the electrodes, and so determine the arrival of a single ion in the substrate.