The Automation folder is a Windows folder called 'boot' on the root of the C: drive.
One way is to use the uninstall policy at Settings > Agents/Plug-ins > All Agents/Settings > Deployment and Migration > Windows > Deployment Automation Folder for Windows (x86) Uninstall.
You could also run a command line on the target machine to remove the Automation folder, as follows.
From NS, click on Manage > Software > Software Catalog.
Search for 'uninstall'. The package for uninstalling the Automation Folder should show up.
Right click > Actions > Edit Software Resource > Package > Command lines. There should be a command line there. Run that command on each client computer.
You can uninstall the whole agent by running 'AexAgentUtil.exe'. Use the command line switch -? to get a list of commands. Check document 'How can I uninstall altiris agent on workstation?' at http://www.symantec.com/connect/forums/how-can-i-uninstall-altiris-agent-workstation