MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
If we are talking about the upper fan over the heatsink then yes of course, this is likely the most important fan of the whole printer. It directs airflow through said heatsink which is clamped directly over the melting zone of the hotend. This is called the "heat brake". It prevents heat from going further up the printhead and makes it possible to perform retraction moves. If the heat was allowed to go further, then eventually the filament would be soft and the feedsystem will compress it inside the guide channel of the printhead, which will result in a colgged extrder mess.
The lower former parts cooling fan with its duct however has to be demounted for the 2-pin connection to be used with the noctua mount. And it's no longer necessary of course.