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Acrobat recently updated the highlighter tool so that it is supposedly a freeform tool, but the free-form capability only works on documents that are scanned. An unfortunate bug in this is that when you try to highlight a scanned PDF, Acrobat also automatically will recognize scanned text and highlight the text, so it's really not a freeform tool at all, because it won't highlight the correct areas like you can with just a regular ol' highlighter pen on your desk.
There are a couple of workarounds: if you highlight regular shapes, like certain proportion of rectangles, squares, and circles, you can use custom stamps to create highlighter shapes that have a blending mode: Document Geek: Highlighting a PDF that contains no fonts. This method looks the nicest, and truly looks like you've actually highlighted something. But while Acrobat stamps are scalable, they only scale proportionally. So a square stamp can only be scaled to a larger or smaller square; never to a rectangle.
Alternatively, if you want more control, you can use Shape commenting tools (Drawing Markups), and then reduce the opacity. That will allow you to, with recision, outline the shape of the building n the page, but because the blending mode is set set to Normal (as opposed to a true Multiply blending mode), it obscures the text a bit. Another issue with this method is that if you use the Sort Comments by Color feature, yo have to set the color in two places: both the stroke and the fill, because Acrobat only sorts comments by stroke color. But if you don't need to sort by color, and aren't too concerned about having the details slightly obscured, then using the Shape tools will be your best bet.
Document Geek: Acrobat Rectangle Tool: Why Do You Disappoint Me So?
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