#!/usr/bin/perl -w

$| = 1;

use strict;
use File::Find;
use FileHandle;
use Net::DNS::ZoneFile;

my $base    = "/chroot/named/master/arpa/in-addr/68/168";
my $out_dir = "/var/tmp/ptr";

find(\&wanted, $base);
exit;

sub wanted {
   return unless ( -f "$File::Find::name" and $File::Find::name !~ m!/com/! );
   return unless ( -f "$File::Find::name" and $File::Find::name !~ m!/net/! );

# Here we get the rootdir as an argument to the wanted function
# then we are going to need to open it as a new filehandle
# so that the module can read it.
   my $root  = shift;
   my $zone  = new FileHandle "$File::Find::name", "r";
   my $out   = join('.', ( split('/', $File::Find::name) )[-1,-2,-3]);
   my $rrset = Net::DNS::ZoneFile->readfh($zone, $root);

# here you were printing to STDOUT, as opposed to OUT
# which is what I assumed you wanted to do.
   open(OUT, ">$out_dir/$out") or die "Cant create $out_dir/$out: $!\n";
   print OUT $_->string . "\n" for @$rrset;
   close(OUT);
}