Thank you for your post, I have modified code according your suggestions and tried to build entire tree:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @arr = (
        'ng1',     ['ng1_1','ng1_2', 'ng1_3', 'ng1_4'],
        'ng2',     ['ng2_1','ng2_2', 'ng2_3', 'ng2_4'],
        'ng3',     ['ng3_1','ng3_2', 'ng3_3', 'ng3_4'],
        'ng1_1',   ['ng1_1_1','ng1_1_2', 'ng1_1_3', 'ng1_1_4'],
        'ng1_1_1', ['ng1_1_1_u1', 'ng1_1_1_u2', 'ng1_1_1_u3'],
        'ng2_1',   ['ng2_1_u1', 'ng2_1_u2', 'ng2_1_u3']
);

my @tree;

for (my $j=0; $j < (@arr/2); $j+=2){
  $tree[$j] = $arr[$j];
  $tree[$j+1] = [ @{$arr[$j+1]} ];
  for (my $i=$j+2; $i < @arr; $i+=2){
    buildTree(\@tree, $arr[$i], [ @{$arr[$i+1]} ]);
  }
}

print "\@arr:\n";
print Dumper @arr;
print "\@tree:\n";
print Dumper @tree;


sub buildTree{
  my ($tree, $parNg, $subNg) = @_;
  for my $treeElement (@{$tree}){
    if (ref $treeElement eq "ARRAY"){
      &buildTree($treeElement, $parNg, $subNg);
    }
    else{
      if ($treeElement eq $parNg){
        my ($index) = grep { $tree->[$_] eq $treeElement } 0..scalar(@
+$tree)-1;
        splice @{$tree}, $index + 1, 0, $subNg;
        #print Dumper \@tree;
      }
    }
  }
}
[download]

but the output is still confusing:

$VAR1 = 'ng1';
$VAR2 = [
          'ng1_1',
          [
            'ng1_1_1',
            [
              'ng1_1_1_u1',
              'ng1_1_1_u2',
              'ng1_1_1_u3'
            ],
            'ng1_1_2',
            'ng1_1_3',
            'ng1_1_4'
          ],
          [
            'ng1_1_1',
            $VAR2->[1][1],
            [
              'ng1_1_1_u1',
              'ng1_1_1_u2',
              'ng1_1_1_u3'
            ],
            'ng1_1_2',
            'ng1_1_3',
            'ng1_1_4'
          ],
          [
            'ng1_1_1',
            $VAR2->[1][1],
            $VAR2->[2][2],
            [
              'ng1_1_1_u1',
              'ng1_1_1_u2',
              'ng1_1_1_u3'
            ],
            'ng1_1_2',
            'ng1_1_3',
            'ng1_1_4'
          ],
          'ng1_2',
          'ng1_3',
          'ng1_4'
        ];
$VAR3 = 'ng2';
$VAR4 = [
          'ng2_1',
          [
            'ng2_1_u1',
            'ng2_1_u2',
            'ng2_1_u3'
          ],
          [
            'ng2_1_u1',
            'ng2_1_u2',
            'ng2_1_u3'
          ],
          'ng2_2',
          'ng2_3',
          'ng2_4'
        ];
$VAR5 = 'ng3';
$VAR6 = [
          'ng3_1',
          'ng3_2',
          'ng3_3',
          'ng3_4'
        ];
[download]

Am I still missing something? Thank you very much.