In a system with particle beams (SEM, FIB) the primary beam brings a certain charge to the sample, but the same time secondary particles (electron, ions) are generated. The net sample current is the sum of the currents of all species (incoming and outgoing). The current is often in the range of pA to nA and a sensitive device is required.
For reducing the effect of the mentioned secondaries (mostly electrons) the sample is usually set to a positive potential (+50...100V).
You can measure the true beam current using a Faraday cup (FC). For some vendors it is integrated in the column to provide good results for lithography or FIB cutting.
A simple FC can be made by drilling a small and deep hole in a sample stub or the sample holder.