Problem:
Error: “The file ‘Manifest Tool.exe’ is not marked for installation” occurs during installation of Cisco AnyConnect client. This generally happens due to a failed upgrade installation of the client..

Solution:
Uninstall any version of the Cisco AnyConnect VPN client if it exist on the system.
Then, edit the registry by following these steps:

• Launch the Registry Editor by typing “regedit” in the search window or box.
• If a dialogue box pops up displaying the following: “Do you want to allow the following program to make changes to this computer?”, Click Yes.
• Browse to the following location: HKEY_CLASSES_ROOT\Installer\Products\
• Within the Products folder, locate and delete the registry key which contains the product information for Cisco AnyConnect.
  1. Go through each key in the Products folder until you find the one for Cisco AnyConnect. For example, the registry key for Cisco AnyConnect is named {D5BA4DB6420F33A4BAA83AD8BF69D037}
  2. Please note that the version of Cisco AnyConnect that you have may display a different registry key name.
• Close the registry editor.
• Install the Cisco AnyConnect client.

** Please make a backup of the registry before deleting or modifying any keys.