for my $i (0 .. $#array) {
    substr($string, $i, 1) = lc substr($string, $i, 1)
        if $array[$i] eq q();
}
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Update: As always, TIMTOWTDI...

$altered_string =
    join q(),
    map {
        my $char = substr($string, $_, 1);
        $array[$_] eq q() ? lc($char) : $char;
    }
    0 .. length $string;
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This probably has all the efficiency of Schlemiel the Painter, but it has some humor value:

!$array[$_] && $string =~ s/(?<=^.{$_})(.)/lc $1/e for 0 .. $#array;
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Silly at best, but it works. :)

This isn't as fun, but doesn't suffer from a lookbehind assertion that grows as the index increases:

!$array[$_] and substr( $string, $_, 1 ) = lc substr( $string, $_, 1 )
    for 0 .. $#array;
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my @array = ("|", "|", "|", "|", "", "|", "|");
print join '', map { my $foo = shift @array ? $_ : lc } split '', 'ASD
+FGHJ';
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This is quite a nice technique. It's worth pointing out though, that it has a side-effect of dismantling @array, so you should make a copy of @array first if you were planning on using the array again.

perl -E'sub Monkey::do{say$_,for@_,do{($monkey=[caller(0)]->[3])=~s{::}{ }and$monkey}}"Monkey say"->Monkey::do'

Worked like a charm, thanks. The first reply for some reason did not and returned all upper case letters. Seems I don't know perl as good as I thought ;].

Any idea how to change it to catch " " instead of ""? Thanks

$string |= join '', map chr( $_ ? 0 : 040 ), @array;
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$array[$_] or substr($string, $_, 1) |= "\x20" for 0 .. $#array;
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$ perl -le'
my $string = "ASDFGHJ";
my @array = ( "|", "|", "|", "|", "", "|", "|" );
print $string;
$string =~ s/(.)/ length $array[ $-[ 0 ] ] ? $1 : lc $1 /eg;
print $string;
'
ASDFGHJ
ASDFgHJ
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