Illustrator :: Highlight Scanned Documents CC X64?

I scanned a worksheet containing chemical structures with VueScan 9.3.14. I tried to use acrobat 11.0.5 along with the highlight tool to highlight parts of a chemical structure. Adobe did not recognize all parts of the chemical structure. Some parts (mostly single covalent bonds between 2 atoms) could be highlighted, but other's could not. Those parts which could not be highlight were important parts I was aiming to use acrobat's highlight tool for. I was hoping if something like the highlight tool in acrobat could be used in illustrator and/or other third party software.