use warnings;
use strict;
use Data::Dumper; # Debug
$Data::Dumper::Useqq=1;
use Text::CSV;

my $file1 = 'in1.txt';
my $file2 = 'in2.txt';
my $outfile = 'out.txt';

my $csv = Text::CSV->new({binary=>1, auto_diag=>2, eol=>$/});

open my $ifh1, '<', $file1 or die "$file1: $!";
open my $ifh2, '<', $file2 or die "$file2: $!";
open my $ofh, '>', $outfile or die "$outfile: $!";

$csv->getline($ifh1); # read and discard header
$csv->getline($ifh2); # read and discard header
$csv->print($ofh, ['col1','col2']); # new header

while ( my $row1 = $csv->getline($ifh1) ) {
	my $row2 = $csv->getline($ifh2);
	die "file1 has more lines than file2" unless $row2;
	
	# do whatever you like to create the output row here
	my $orow = [@$row1, @$row2]; # example: join the two rows
	
	print Dumper($row1, $row2, $orow); # Debug
	$csv->print($ofh, $orow);
}
die "file2 has more lines than file1" unless eof($ifh2);

close $ifh1;
close $ifh2;
close $ofh;

$csv->eof or $csv->error_diag;