Unless you configure your Brother MFC scanner to compile multiple pages into a single scanned document, you will have dozens if not hundreds of unique files to save.

VueScan will scan several pages and save them to a PDF file. It's fairly simple to use once you've figured out the hooks in the UI.

If you need to scan multiple pages, SwiftScan lets you save them as a single document with Multi-Page scans. Choose to save your file as a JPEG or PDF.