I am trying to remove the out of date and duplicate entry from Server. what is the easy way to clean it?

Loign SEPM --> Admin --> Servers-->

Click the local site and edit Site Properties

In General tab you will be having options

Delete clients that have not connected for "_n_" days

You can set the time according to your old date time period(eg- 1 day). By default time is 30 days

https://www-secure.symantec.com/connect/forums/how-fix-duplicate-entries-particular-group

Duplicate SEP clients appear in the Symantec Endpoint Protection Manager console

https://www-secure.symantec.com/connect/articles/duplicate-sep-clients-appear-symantec-endpoint-protection-manager-console

How to configure the number of days after which inactive clients will be deleted from the SEPM database on SEPM 12.1 RU1