my $last_match=0;
while ($wholefile =~ /(pattern for table)/){
   $newfile .= substr($wholefile, $last_match, ($last_match - $-[0]));
   $newfile.=eval{sub($1)}; # I think this is what you want to do
   #of course it will always return 0, 
   #but that's what you have in the regex above.
   # perhaps you meant $newfile.= "sub($1)";
   $last = $+[0];
}