Wait, are you feeding the paper in through the document feeder, and hitting to Scan only once, but getting 3 separate files?
Is this scan to email, or scan to PC?
If you are scanning from the glass and doing 3 scans, you get 3 files.
If you are scanning to jpg, you get 3 files.
If you scan using the feeder, and use pdf, you get one file , to set this go to Machine Status > Tools > Default Settings > Scan Defaults > File Format