There is a separate glass that is used by the document handler this is why your copies do not have any lines when using the glass itself. Please take a look at this article on how to clean the glass used by the feeder.
I'm getting a single line down each page I copy on my Work Centre 3615 printer. However, it only happens when I use the sheet feeder at the top of the machine. There is no line if I copy something by putting a single sheet down on the glass window. So, something seems to be amiss with the sheet feeder. How do I fix (or clean) it?