Abstract: A method of operating a particle beam system includes determining a deflection amount and a deflection time of a beam deflection module connected to a data network. The method also includes determining an un-blank time of a beam blanking module connected to the data network, and determining a blank time of the beam blanking module connected to the data network. The method further includes generating a data structure which includes plural data records, wherein each data record includes a command representing an instruction for at least one of the modules, and a command time representing a time at which the instruction is to be sent to the data network. In addition, the method includes sorting the records of the data structure by command time, and generating a set of digital commands based on the data structure. Moreover, the method includes sending the digital commands of the set to the network in an order corresponding to an order of the sorted records.