Highlight only works with actual text so you'd have to run the scanned PDF through OCR (Paper Capture in Acrobat). If you have Acrobat 6.01 I think you could do something similar to highlight using the Tools>Advanced Editing>Drawing then pick the rectangle tool. You can make this look similar to a highlight effect using the opacity property control. The important differecne is that the highlight text effect is behind the text whereas the rectangle will be in front of the scanned page - hence the need for an opacity property.
Hope this helps