#! perl
use strict;
use warnings;
use List::Util qw(any);

my $file = do { local $/; <DATA>; };        # Slurp the whole file into a string

# Make a hash that maps each word to its word count in the file
my %words;
 ++$words{lc $_} for split /\W+/, $file;

# Construct a regular expression to match each word which appears at least twice
my $re;

if (any { $_ > 1 } values %words)
{
    my $str = '\\b' . join('\\b|\\b', grep { $words{$_} > 1 } keys %words) . '\\b';
    $re = qr{($str)}i;
}

$words{$_} = 0 for keys %words;             # Re-set the word counts to zero

# Mark the second and subsequent occurrences of each word
$file =~ s{$re}{ $words{lc $1}++ ? "*$1*" : $1 }eg if $re;

print $file;