You're not untainting the variable in-place, your call to the function should read as follows:

    $name = untaint($name);
    $siteName = untaint($siteName);
    open (FILE,">/$directory/tmpl/$name.tmpl");
        print FILE $content;
    close(FILE);

sub untaint {
    my $var = $_[0];
    unless ($var =~ m/^(\w+)$/) { #allow filename to be [a-zA-Z0-9_]
        die("Tainted");
    } 
    return $var;
}
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I've asked a question about another topic here, but I think you can find the answers quite useful for your tainting doubts.