... operate with only file locations ... not ... texts of file in program ...

Opening files for reading in the "normal" way (as opposed to the ramdisk-ish approach used for convenience in the example code) is straightforward and is well described in the open and perlopentut docs. Maybe also take a look at Files and I/O in perlintro.

... print the output in other file.

This merely involves opening a write filehandle (see docs referred to above) inside the Perl script and print-ing to this filehandle rather than to STDOUT by default, or else redirecting standard output from the Perl script as a whole to a file via the OS command line (see your OS docs regarding I/O redirection).

Update: Minor wording changes to (hopefully) enhance clarity.