XenApp Developer Network released the XenAppPrep Tool at Summit 2008 in the end of October. In the past, the ability to clone or stream a Citrix XenApp server required extensive customization and scripting. The XenAppPrep tool can be used to generalize a XenApp installation and make this process extremely simple and straightforward.
Simply download the XenAppPrep and install with default options.
After the installation is finished and your server is ready to be cloned run the XenAppPrep.exe if cloning with WDS and then ofcourse Sysprep or use XenAppPrep.exe /PVS if you gonna build a Provisioning Server vDisk.