Simplest way is to rename your database via Project ‘yourproject’ → Settings → tab Configuration → tab Database → Database name. Now press F5 and you will get a popup
That will of course be empty.
Another way, if you have your project set on database type “Built-in database”, is indeed to clean your project’s directory ‘deployment’. Or more precise: deployment\data\database\hsql\<yourdatabasename>. Have a look at Mendix’ behavior there. Always nice to have a grasp of Mendix’s inner workings.
These both require manual deletion. If you want this as an automated step, your will probably have to built your own progress script to take care of cleaning data upon start, or you can create a after-startup routine in your app that checks if your app is running locally, and if so remove the data that you need to have removed.