my ($start, $stop) = (qr '#ifdef|#if|#ifndef|#else', qr '#endif');

open(file1,$file) or die "Error opening input: " . $!;
open(file2, ">$filea") or die "Error opening input: " . $!;

while (<file1>) {
   if (/$start/ .. /$stop/) {
    next;    
   }
   else
   {
     print file2 $_ ;
   }
}