Something like this might work:

#!/usr/bin/perl
use strict;
use warnings;

my $fileOne = $ARGV[0];
my $fileTwo = $ARGV[1];
my $x = 0;


my $count = 0;
open (my $one, "<", $fileOne);
while (<$one>)
    {
        $count += 1;
    } 

open ($one, "<", $fileOne);
open (my $two, "<", $fileTwo);
open (my $out, ">", "outputfile.txt");

for ($x = 0; $x < $count; $x += 1)
    {
        my $lineOne = <$one>;
        my $lineTwo = <$two>;

        print $out "$lineOne" if $lineOne eq $lineTwo;
    }
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