The problem is about undef $/; delay it until you want to slurp the file

foreach ( grep( /^.*\.xml$/, readdir(DIR) ) ) {
  print "Pls enter Section level value for $_ :  ";
  chop( $seclev = <STDIN> );
  {
    local $/;
    open( FIN, "<$_" ) or die("$_ is not opened\n");
   ..  
}
}
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