1. Unregistered all the versions of ASP.NET with command "C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis –ua".
2. Deleted the ASPNET account from "Local Users and Group – Users".
3. Then registered ASP.NET 2.0 with IIS using "C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis –i".
4. Gave permissions to the ASPNET account using "C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis –ga machinename\ASPNET".
5. Reset the IIS and that resolved the issue for ASP.NET 2.0.