To clear Site data, select the Site you want to wipe clean from the top menu bar, as shown below.
One you select Clear Current Site Data you are given the option of which data you would like to delete.
Note: if you wish to delete data from a Production site, one workaround is to first cancel all active subscriptions, at which point you can edit the Site and place it back in to Test Mode.
Site data can be deleted in bulk for sites that are in Test Mode only. When you are working with a Site that is in Test Mode, the following header on will be shown on your Dashboard: