delete_key_list = []
for key in bucket.list(prefix='/your/directory/'):
    delete_key_list.append(key)
if len(delete_key_list) > 100:
    bucket.delete_keys(delete_key_list)
delete_key_list = []
if len(delete_key_list) > 0:
    bucket.delete_keys(delete_key_list)
Amazon S3 boto - how to delete folder?