Test Case should not be part of Test Plan. is it possible to do that?

You can use the destoywi[^] command to permanently remove any Work Item from TFS. I have the below code snippet in a bat file that I use when required.

@ECHO OFF
ECHO Please type the IDs :

set /p id=

cd c:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE

witadmin destroywi /collection:"http://<your tfs="" server="">:8080/tfs/<your tfs="" collection="" name="">" /noprompt /id:%id%

PAUSE</your></your>