Dear Mohammad,
you can use the command line post processing tools bundled with FLUKA. (See: 3.5. Accessing results — FLUKA Manual)
By default these programs work in an interactive mode, but it is possible to prepare the answers beforehand in a text file, like:
in.txt:
<input_file>001_fort.xx
<input_file>002_fort.xx
<output_file>
Then you can pipe this file into the post processing tool, for example:
usbsuw < in.txt
Cheers,
David