WordPress mysql table double prefixes

1) In order to check what kind of prefix used by current installantion you can goto wp-config.php in a root directory and find line with $table_prefix = 'PREFIX_HERE'; variable

2) Backup the DB before making any action!

3) Additionally check if other tables with different prefixes/name_patters are not used by badly-written 3rd party plugins. They may not follow a good-practice:

Do not hardcode the WordPress database table prefix (usually “wp_”)
into your Plugins. Be sure to use the $wpdb->prefix variable instead.

4) Right after this done you can drop all tables using a UI mysql admin panel or using more advanced way:

a. Generate a DELETE query programmaticaly:

SELECT CONCAT( 'DROP TABLE ', GROUP_CONCAT(table_name) , ';' ) 
    AS statement FROM information_schema.tables 
    WHERE table_schema="YOUR_TABLE_NAME" AND table_name LIKE 'WORDPRESS-PREFIX_%';

b. Perform generated result.