It's not the scanner that's creating the layers. It's the scanning software. Here's an example: http://office.microsoft.com/en-us/help/optimize-your-scanning-for-speed-image-quality-or-ocr-results-HA001102160.aspx
You don't have to take my word for it. I'm not a graphics expert. Do it yourself. Scan an image for a PDF file. Your presets (in the software) should have OCR on. Open your new PDF and see the layers.
PS It has been shown that there are NO OCR objects in that PDF file!