In order to uninstall the Enterprise Console from an end user machine you can follow this manual https://www.paessler.com/manuals/prtg/uninstall if your want to uninstall the Console from the PRTG server it would be different.

The Enterprise Console comes as part of the whole PRTG installation, it cannot be uninstalled independently but it can be disabled. You can go to the configuration settings of the app, and uncheck the option to start with windows, and then exit the app. That way it will be disabled and you won't see the pop-ups anymore. You can install the PRTG desktop instead and use that one in the same server if needed.

The new PRTG Desktop app has the same functionalities than the older Enterprise Console, but some settings may look different, therefore if you have questions about the usage of the new app please refer to the manual in this link https://manuals.paessler.com/prtgdesktop/prtgdesktop.pdf