how to clear the database

Here are the ones you NEVER touch.

wp_users
wp_usermeta
wp_posts
wp_postmeta
wp_post2cat
wp_options
wp_links
wp_linkcategories
wp_comments
wp_categories

Any others you should ’empty’. That keeps things good in case they are used but frees up space.
How to empty tables:
http://www.tamba2.org.uk/wordpress/empty-drop/

Backup your database before doing anything

The risk here is yours.