Gold marks on the reference block allow the system to calibrate beam deflection and distortion. The Faraday cup is used for measuring beam current. It is simply a hole from which secondary electrons cannot escape. Do you know who Michael Faraday was? Better look him up, and then ANSWER THIS QUESTION. The positions of markers and Faraday cups are stored in the EBPG, so you need only indicate which sample chuck you are using.