Keep in mind: If you use the POP email protocol, the email will only be removed from Mozilla Thunderbird and remain on the mail server. With IMAP, email is deleted on both Mozilla Thunderbird and the mail server.
It's very easy to remove email in Mozilla Thunderbird, here are the steps to follow.
1. Open Mozilla Thunderbird.
2. Open Inbox, right-click on the email you want to delete and then click on Delete Message.
And you just deleted that email.