You aren't copying the files with Perl, you are copying the files fith a DOS command which is invoked from Perl.
If your goal is to eliminate the file of zeroes, I would suggest a perl routine to open an input file, copy it line by line to a provided output filehandle, and then close the file. To insert the zeroes, you can simply write to the output filehandle .... except you may need to reopen it in binary mode. Maybe printing "\x00" .. the string containing a single byte with the value 00 ... will work, you can give it a try.
P.S. What does this have to do with "accessing randon number from perl script"?
As Occam said: Entia non sunt multiplicanda praeter necessitatem.
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