Please give me some tips
1. use strict; use warnings;. Always. Doing so will help make your life easier when writing code.

2. When posting code on PM, using the __DATA__ handle makes it easier for others to reproduce what your seeing. One file, one click. This in turn makes it easier for others to respond and assist you.

in the 2nd row, I am not sure how to increment the column Number cNum based on the previous column span's value That's one way you could do it, though in my opinion, not the best approach...
(Since you asked for tips, I'll give you a hint and leave you to work it out.) How about this: (see comment)

#!/usr/bin/perl
use strict;
use warnings;

{
    local $/='<tr>';
    while (my $line = <DATA>){
        my $i=0;

        while ($line =~ m/<tc>/) {
            $line =~ s!<tc>!'<tc cNum="'.++$i.'">'!ie;
            #why not insert another substitution in here that handles 
+the case <tc (colspan="\d+")> ...
        }
        print $line;
    }
}

__DATA__
<tr><tc>1</tc><tc>2</tc><tc>3</tc></tr>
<tr><tc colspan="2">1and2</tc><tc>3</tc></tr>
<tr><tc>1</tc><tc colspan="2">2and3</tc></tr>
<tr><tc>1</tc><tc>2</tc><tc>3</tc></tr>
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