The bin file is your output of the current system spi content by the FPT tool, the cleaning method aplies to the full spi or ME region, full spi is recommended, its described in the guide.
The output result file is the cleaned ME, using the same or near up version image in the repository matching the current ME version in the system now.
This operations requires the access to the spi regions, also in the guide, other than that only by using a programmer.
If you already read the guides you wont be doing this questions…so again, read and learn.