Abstract: A host computer with a FPGA is communicatively coupled to a configuration computer via a communication network. The host computer receives target configuration data from the configuration computer in encrypted form. A scanner module that is associated with the host computer decrypts the target configuration data and scans it for malicious code. The module writes the target configuration data to the fabric area of the FPGA and thereby configures the FPGA accordingly, to enable execution of a target array application. The scanner module is associated with the host computer by being implemented as trusted execution environment, or as an on-array-processor.