Ok, I had to go look for a moment.
On mine part of the Brother Utilities app has an item called Control Center 4. It has selections for "Image", "OCR", "email", "file".
In order for this machine to scan off of the auto feed I simply load it to the machine, a light on the machine turns on. I can scan it from the machine itself OR I go to the CC4 program and hit "file", in my own case I changed preferences to ask me where I want to save and name. Once I do that and hit enter it just proceeds with the operation.
There is no where else in Windows that I can select to do a scan aside from lifting the top. Otherwise, in Windows and separate of the CC4 app I can only do that manner of scan and a traditional print. I can do both of those...