my @values = (undef, $var1, $var2, $var3);
my @where;
my $sql = 'select * from table';

my @defined_values;
foreach my idx (1..3) {
  if defined $values[$idx] {
    push @where, qq(column$dx = ?);
    push @defined_values, $values[$idx];
  }
}

$sql = $sql . ' where ' . join(' and ', @where);

my $sth = $dbh->prepare_cached($sql);
$sth->execute(@defined_values);