That's not the hard part. The hard part is doing "the right thing" if the files do not have the same number of lines. Oh, and if these were arrays - you might want to look at tye's Algorithm::Loops - specifically mapcar. FWIW - you can read a file into an array pretty easily using the syntax my @array = <FILEHANDLE>; # just remember you have slurped the entire file into memory.

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

my $file1 = $ARGV[0] || 'file1.txt';
my $file2 = $ARGV[1] || 'file2.txt';
open (FILE1, '<', $file1) or die "Unable to open $file1 for reading : 
+$!";
open (FILE2, '<', $file2) or die "Unable to open $file2 for reading : 
+$!";

while ( <FILE1> ) {
    chomp;
    my $foo = <FILE2>;
    $foo = 'N/A' if eof FILE2;
    print join "\t" , $_ , $foo;
    print "\n";
}
while ( <FILE2> ) {
    chomp;
    print join "N/A\t$_\n";
}
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