If I understand correctly what you are wanting to do .. this is how I would do it.

Have fun !!

-Kiel R Stirling

#!/usr/bin/perl -w

use strict;
use IO::File;

my $output = pop @ARGV;
my @merge;
for my $file (@ARGV) {
        my $input_fh = IO::File->new($file);
        die "failed to open $file\n"
                unless defined $input_fh;
        $merge[$.-1] .= $_
                while (defined ($_ = <$input_fh>) and chomp);
        $input_fh->close;
}

my $output_fh = IO::File->new("> $output");
die "failed to open $output\n"
        unless defined $output_fh;

$" = "\n";
print $output_fh "@merge";
$output_fh->close;
[download]

./merge.pl file1 file2 file3 output_file