Delete Custom Content Type Content with Custom Fields
You could use node_delete or node_delete_multiple to do this:

// Retrieve all nids for your custom content type.
$result = db_query("SELECT nid FROM {node} WHERE type = :node_type", array(":node_type" =&gt; "&lt;YOUR_CONTENT_TYPE&gt;"))
  -&gt;fetchAll();

// Delete all nodes.
foreach($result as $nid) {
  node_delete($nid);
}

// You should also be able to use node_delete_multiple().
// node_delete_multiple($result);