Sorry here is the perl code.

#!/bin/perl5.8.6

$flag = open(file1, "main.c");
$flag2 = open(file2, ">main_out.c");

if(flag && flag2){
while(!eof(file1)){
  $line = <file1>;
  $/ = undef;
  $_ = <file1>;
  s#(/\*.*?\*/)|//[^\n]*|("(\\.|[^"\\])*"|'(\\.|[^'\\])*'|.[^/"'\\]*)#
+defined $2 ? $2 : ""#gse;
  print file2 ($_);
}
}
 
 close(file1);
 close(file2);
[download]

To start with: After entering the loop you are reading the first line ($line = <file1>) and throw it away (because $line is never be used again), so from this alone we can conclude that you won't recognize a comment which starts in the first line. You would have found this immediately, if you had included use strict; use warnings FATAL => 'all'; in your code.
There are more problems in your code, but I suggest you first enable strict and warnings, then try to improve the code (based on what I told you above), and if you still can't get it running, post your updated code here.
-- 
Ronald Fischer <ynnor@mm.st>

Thanks Ronald, got my mistake and it is working fine. Im new into perl learning a lot thanks for your help