I have tried the below method ,Its worked for me .
//Get the Session
Session session = pfcGlobal.GetProESession();
//Get the Active Model
Model mod=session.GetCurrentModel(); //Rename the Model in Session
//Rename (String NewName, /*optional*/ Boolean RenameFilesToo) from Jlink Doc
Note from PTC
If the models are retrieved from a directory other than the current working directory the Models are renamed only in the session and not on disk