here is my code:

  $ctr=0;
  while(/(<table>[^\000]*?<\/table>)/){
    $text=$1;
    while($text=~/<table>/){
      $tag=$&;
      $ctr=$ctr+1;
      $tag=~s/(<table)/\1$ctr/;
      $text=~s/<table>/$tag/;
    }
    $text=~s/(<table)$ctr>/\1_level$ctr>/g;
    $text=~s/(<\/table)>/\1_level$ctr>/g;
    $ctr=0;
    $text=~s/(<table)[0-9]+>/\1>/g;
    $text=~s/(<\/?)(thead|tbody)([^>]*)?>//g;
    $text=~s/(<\/?)(th)([^>]*)?>/$1td>/g;
    while($text =~ /<a href="([^"]*)">[^\000]*?<\/a>/){
      $href = $1;
      $class = "";
      if($href =~ /^http/i){  $class = "http";}
      if($href =~ /^www/i){   $class = "nohttp";}
      if($href =~ /^mailto/i){$class = "mailto";}
      if($href =~ /^ftp/i){   $class = "ftp";}
      if($class eq ""){
        $text =~ s/<a href="([^"]*)">([^\000]*?)<\/a>/\2/;
      }else{
        $text =~ s/<a href="([^"]*)">([^\000]*?)<\/a>/<remotelink href
+class="$class" href="\1" >\2<\/remotelink>/;
      }
    }
    s/<table>[^\000]*?<\/table>/$text/;
  }

  # Remove table and img tags inside table if an <img /> tag was encou
+ntered
  while (/<table_level(2|3)>[^\000]*?<\/table_level\1>/) {
    $table2=$&;
    if ($table2 =~ /<img /) {
    # Remove all table tags including <img /> tag
    $table2=~s/<\/?(table_level(2|3)|tr|td)(\s+[^>]*)?>|<img\s+[^>]*\/
+>//g;
    s/<table_level(2|3)>[^\000]*?<\/table_level\1>/$table2/;
    }  
    else {
      $table2=~s/(<\/?table_level\d)/$1_temp/g;
      s/<table_level(2|3)>[^\000]*?<\/table_level\1>/$table2/;
    } 
  }
  s/(<\/?table_level\d)_temp/$1/g;

  # Extract table inside table if no <img /> tag was encountered
  # inside the inner table.
  while (/(<table_level1>[^\000]*?<\/table_level1>)/) {
    $table1=$1;
    #$table2="";
    $table="";
    while ($table1=~ /<table_level2>([^\000]*?)<\/table_level2>/) {
      $table2=$1;
      $table=$&;

      # Extract inner table and place it after the second level table 
+ 
      $extracted_table3="";
      while ($table2 =~ s/(<table_level3>[^\000]*?<\/table_level3>)//)
+ {
        $extracted_table3="$extracted_table3\n$1"; 
      }

      $table2=~s/<table_level2>([^\000]*?)<\/table_level2>/$table$extr
+acted_table3/g;
      #$table2=~s/(<table_level2>[^\000]*?<\/table_level2>)/$1$extract
+ed_table3/g;
      s/(<table_level2>[^\000]*?<\/table_level2>)//;
      #$table2=~s/(<\/?table)_level2/$1_2/g;
    }
    $table1=~s/<table_level2>([^\000]*?)<\/table_level2>//;
    $table1=~s/<table_2>([^\000]*?)<\/table_2>//;
    $table1=~s/(<\/?table)_level1/$1/g;
    s/<table_level1>[^\000]*?<\/table_level1>/$table2$table1/;
  }
  s/(<\/?table)_(level\d|\d)/$1/g;
[download]

And here is my sample data

<table>
    <tr>
        <td>
            <table>
                <thead>
                    <tr>
                        <th>Vill</th>
                        <th>Hi</th>
                        <th>Au</th>
                    </tr>
                </thead>
                <tbody>
                    <tr>
                        <td>Aix</td>
                        <td>40</td>
                        <td>27</td>
                    </tr>
                    <tr>
                        <td>Freib</td>
                        <td>30</td>
                        <td></td>
                    </tr>
                    <tr>
                        <td>Gdan</td>
                        <td>20</td>
                        <td>13</td>
                    </tr>
                    <tr>
                        <td>Gd</td>
                        <td>44</td>
                        <td>14</td>
                    </tr>
                    <tr>
                        <td>Gren</td>
                        <td>33</td>
                        <td>22</td>
                    </tr>
                    <tr>
                        <td>Karl</td>
                        <td>26</td>
                        <td></td>
                    </tr>
                    <tr>
                        <td>La</td>
                        <td>31</td>
                        <td>18</td>
                    </tr>
                    <tr>
                        <td></td>
                        <td>30</td>
                        <td>20</td>
                    </tr>
                    <tr>
                        <td>Lyon</td>
                        <td>41</td>
                        <td>19</td>
                    </tr>
                    <tr>
                        <td>Man</td>
                        <td>22</td>
                        <td></td>
                    </tr>
                    <tr>
                        <td>Mar</td>
                        <td>32</td>
                        <td>18</td>
                    </tr>
                    <tr>
                        <td>Mar</td>
                        <td>17</td>
                        <td>13</td>
                    </tr>
                    <tr>
                        <td>Mon</td>
                        <td>36</td>
                        <td>26</td>
                    </tr>
                    <tr>
                        <td>Mul</td>
                        <td>30</td>
                        <td>45</td>
                    </tr>
                    <tr>
                        <td>Mun</td>
                        <td>28</td>
                        <td>23</td>
                    </tr>
                    <tr>
                        <td>Nice</td>
                        <td>41</td>
                        <td>17</td>
                    </tr>
                    <tr>
                        <td>Nims</td>
                        <td>34</td>
                        <td>25</td>
                    </tr>
                    <tr>
                        <td>Nio</td>
                        <td>29</td>
                        <td>21</td>
                    </tr>
                    <tr>
                        <td>Orleans</td>
                        <td>32</td>
                        <td>17</td>
                    </tr>
                    <tr>
                        <td>Pad</td>
                        <td>36</td>
                        <td>20</td>
                    </tr>
                    <tr>
                        <td>Paris</td>
                        <td>24</td>
                        <td>29</td>
                    </tr>
                    <tr>
                        <td>Perk</td>
                        <td>38</td>
                        <td>29</td>
                    </tr>
                    <tr>
                        <td>Poit</td>
                        <td>27</td>
                        <td>24</td>
                    </tr>
                    <tr>
                        <td>Prag</td>
                        <td>26</td>
                        <td>16</td>
                    </tr>
                    <tr>
                        <td></td>
                        <td>23</td>
                        <td>14</td>
                    </tr>
                    <tr>
                        <td>Ren</td>
                        <td>30</td>
                        <td>18</td>
                    </tr>
                    <tr>
                        <td>Rot</td>
                        <td>36</td>
                        <td>27</td>
                    </tr>
                    <tr>
                        <td>Rou</td>
                        <td>45</td>
                        <td>22</td>
                    </tr>
                    <tr>
                        <td>Saint</td>
                        <td>33</td>
                        <td>20</td>
                    </tr>
                    <tr>
                        <td>Salon</td>
                        <td>33</td>
                        <td>18</td>
                    </tr>
                    <tr>
                        <td>Sev</td>
                        <td>63</td>
                        <td>29</td>
                    </tr>
                    <tr>
                        <td>Sop</td>
                        <td>19</td>
                        <td>8</td>
                    </tr>
                    <tr>
                        <td>Stra</td>
                        <td>28</td>
                        <td>26</td>
                    </tr>
                    <tr>
                        <td>Stut</td>
                        <td>26</td>
                        <td></td>
                    </tr>
                    <tr>
                        <td>logne</td>
                        <td>22</td>
                        <td>11</td>
                    </tr>
                    <tr>
                        <td>lon</td>
                        <td>31</td>
                        <td>22</td>
                    </tr>
                    <tr>
                        <td>use</td>
                        <td>28</td>
                        <td>17</td>
                    </tr>
                    <tr>
                        <td>Ts</td>
                        <td>29</td>
                        <td>22</td>
                    </tr>
                    <tr>
                        <td>Val</td>
                        <td>36</td>
                        <td>23</td>
                    </tr>
                    <tr>
                        <td>Zur</td>
                        <td>29</td>
                        <td>22</td>
                    </tr>
                </tbody>
            </table>
        </td>
        <td>
            <table>
                <tr>
                    <td><span><strong>Legend</strong></span></td>
                </tr>
                <tr>
                    <td>
                        <table>
                            <thead>
                                <tr>
                                    <th>head1</th>
                                    <th>head2</th>
                                </tr>
                            </thead>
                            <tbody>
                                <tr>
                                        <td>bon</td>
                                        <td></td>
                                        <td>0 / 25</td>
                                </tr>
                                <tr>
                                        <td>Ton</td>
                                        <td></td>
                                        <td>25 / 50</td>
                                </tr>
                                <tr>
                                        <td>Don</td>
                                        <td></td>
                                        <td>50 / 75</td>
                                </tr>
                                <tr>
                                        <td>Con</td>
                                        <td></td>
                                        <td>75 / 100</td>
                                </tr>
                                <tr>
                                        <td>Trs</td>
                                        <td></td>
                                        <td> 100</td>
                                </tr>
                            </tbody>
                        </table>
                    </td>
                </tr>
            </table>
        </td>
    </tr>
    <tr>
        <td colspan="2"></td>
    </tr>
    <tr>
        <td colspan="2">This is a sample content</td>
    </tr>
    <tr>
        <td colspan="2"></td>
    </tr>
    <tr>
        <td colspan="2">Site : <a href="http://www.yahoo.com" target="
+_blank">www.yahoo.com</a></td>
    </tr>
</table>
[download]

The output should be like, if a table is consists of 3 levels. the level 2 should be at the top of level 1 then level 3 should be at the bottom of level 2.

The output will be:

level2

level3

level1

If there will be a table greater than the 3rd level or the deepest level, it will be outputted at the bottom of the 3rd level.

Example

level2

level3

level4

level5

level6

level7

level8

level1

Hope I explained it well.

Seriously, this is better achieved using one of the HTML::Parser modules. For example take a look at HTML::TokeParser

use strict;
use warnings;
use HTML::TokeParser;
my $p = HTML::TokeParser->new("file.html") # your source file
     ||die "Cant open: $!";
my $depth=0;
while (my $token = $p->get_token) { 
   if (lc(${$token}[1]) eq "table"){
      $depth++ if (${$token}[0] eq "S");
      $depth-- if (${$token}[0] eq "E");
   print "$depth\n";
   }
}
[download]

Try out the code above and see where it takes you
print "Good ",qw(night morning afternoon evening)[(localtime)[2]/6]," fellow monks."