#! perl
use strict;
use warnings;

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 $str = join '|', grep { $words{$_} > 1 } keys %words;
my $re  = qr{($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;

print $file;

__DATA__
To be or not to be; that is to be the question.
Is that the question? Yes!