use Data::Dumper;

my @array1 = ('foo', 'bar', 'baz');
my @array2 = ('foo2', 'bar2', 'baz3');

my $hashref = {};
foreach my $a(\@array1, \@array2){
    my $tmpref  = $hashref;
    foreach my $k(@$a){
        $tmpref->{$k} = {};
        $tmpref = $tmpref->{$k};
    }
}

print Dumper $hashref;

__OUTPUT__

$VAR1 = {
          'foo2' => {
                      'bar2' => {
                                  'baz3' => {}
                                }
                    },
          'foo' => {
                     'bar' => {
                                'baz' => {}
                              }
                   }
        };