Best way is to create a new database. change wp-config.php file to point to this new one and let wordpress install itself and then reload the theme post install. That way, you retain the old one just in case you need the sample data for reference.
If you are talking about development environment, above way is a good way to go about it. This way you can instantly switch back and forth between the sample data and the clean install by just changing the db name in wp-config.php ( I usually have same user assigned to both DBs).
And when you feel you are done with sample data completely, just delete the old DB. No manual deletion of posts, pages etc. required. Hope this makes sense. Thanks