If you want to remove email from Mozilla Thunderbird, you can easily do it but if you use IMAP, the email will only be removed from your Thunderbird email client and the email will be keep on your mail server.
If you use POP settings, then email will be removed from both your Thunderbird Email Client and the Main email server.
1. Open Mozilla Thunderbird.
2. Open Inbox and right click on the email you want to delete and then click on the "Delete Message" option.