Charging in the ion beam image appears as (growing) black areas. The reason is illustrated in the right schematic: A positive charge (from the positive gallium ions) builds up at the surface in non-conductive samples due to gallium ion implantation and emission of electrons which also creates a positive net charge. The signal that creates the ion beam image is secondary electrons (we saw that earlier in the ion–solid interaction section). The secondary electrons have a negative charge and are back attracted to the now positively charged sample and do not reach the detector. The image appears dark since no signal is detected.

The charge can be compensated by using the SEM column as a floodgun. The negative electron beam is scanned over the sample while imaging with the ion beam. The electron beam compensates the build up of positive charge. This sample neutralisation allows the ion-beam-created secondary electrons to escape and reach the detector. Charge neutralisation can also be used when patterning and allows milling of semiconducting- and non-conductive samples. Low energy electrons are conventionally used for this.