I have created some list of properties under the TestCase. For example look at the following screenshot.
Finally I got the answers for removing Project, Testsuite and Testcase custom properties. Here are the scripts.
testRunner.testCase.testSuite.project.removeProperty( "Project_Level_Property" );
testRunner.testCase.testSuite.removeProperty( "Testsuite_Property" );
testRunner.testCase.removeProperty( "Testcase_Property" );
If any other way is there, please let me know friends.