I have created a cluster and few application servers or clones inside the cluster. I wonder if there is a way to rename the servers or will i have to create them all over again with required names?
Yes you can do that. If you are referring to WAS Liberty (which I don't think you are based on your question) it is as simple as renaming a server directory (if they are not part of the collective). If they are part of the collective, you would need to remove the server and re-join it (since the join establishes a security identity which includes the server's directory name).
If you are referring to WAS traditional there are some sample scripts which show https://www.ibm.com/developerworks/websphere/library/samples/SampleScripts.html
There's an old, but still accurate, blog post on how to use those samples: http://biounix.blogspot.com/2009/01/how-to-change-websphere-app-server-name.html?cm_mc_uid=99708927853414425183337&cm_mc_sid_50200000=1487776733