Solution
1. Use this link to prepare the image via GUI
http://blogs.msdn.com/b/petersad/archive/2009/12/17/sql-server-2008-r2-sysprep-step-by-step.aspx
2. copy the contents on SQL Server ISO on the root C:\xxxxxx
3. complete the image using configuration.ini ( scripted install )
you will have to modify your setupcomplete.cmd in C:\windows\setup\scripts folder
4. once setup is finish you can run a batch file to delete the setup folder .
any issues let me know