Open your Trash or Spam folder from the left sidebar. A bar at the top of the thread list shows how many threads are in the folder, along with an Empty trash now (or Empty spam now) button. Click it to permanently delete everything in the folder from your mail server.
This can't be undone. Emptying the folder removes the messages from your email account, not just from Mailspring.
If you only want to remove a few messages, select them while viewing the Trash folder and press Delete to remove them permanently.
Pro Features