The Problem was solved.
Remove liferay portal (tomcat server) folder and replace with new one. When we start the server it will go to deploy folder for registration then at that time paste the XML file received after downloading Liferay 6.1 Enterprise Edition in Deploy folder of liferay portal (tomcat server) folder. Then it will get registered.
06:25:59,822 INFO [AutoDeployDir:84] Creating missing directory /EnterpriseEdition/newportal/deploy
06:25:59,824 INFO [AutoDeployDir:105] Auto deploy scanner started for /EnterpriseEdition/newportal/deploy
26 Mar, 2012 6:26:07 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
26 Mar, 2012 6:26:07 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
26 Mar, 2012 6:26:07 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 47197 ms
06:26:13,343 INFO [AutoDeployDir:167] Processing license-portaldevelopment- developer-6.1-triallicenses.xml
06:26:13,400 INFO [LicenseAutoDeployListener:?] Copying license for /EnterpriseEdition/newportal/deploy/lic ense-portaldevelopment-developer-6.1-triallicenses.xml
06:26:13,470 INFO [LicenseManager:?] Portal Development license validation passed
06:26:13,471 INFO [a:?] License registered
09:11:02,518 INFO [PluginPackageUtil:1409] Checking for available updates
09:11:02,519 INFO [PluginPackageUtil:1453] Finished checking for available updates in 0 ms
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