Typically they use something like column chromatography on a homogenate sample of apple (basically mushed up apple) and then you could identifiy the polyphenol containing fractions (I think one of the more common classes of polyphenols in apples are the flavanols).
You might also be able to extract certain polyphenols from a homogenate into a solvent like acetone but it may also bring other things with it.
Just be careful if you are trying to do this for human consumption because I never trust things that have come into contact with laboratory glassware/solvents.