Hello,
the FreeMASTER can only communicate with the target MCU in runtime. It does not have any JTAG/flash-programming features.
FreeMASTER can help to load the S-Record file and pass its content in small chunks to the MCU application for further processing (or even flashing), but the flashing itself needs to be implemented by the MCU application. See doc/flash_prog.pdf document included in the installation for more details about this feature.
Regards,
Michal