Probably the most effective way to ensure proper sanitation of a counterflow chiller is to use Powdered Brewers Wash, details of which can be found on
our sanitation page. This product is designed specifically for clean-in-place applications in the brewing industry, where you cannot see the surfaces you are cleaning. It is extremely effective at removing the organic compounds left behind by beer and beer wort. Another good cleaner to use here is OxyClean. Both of them need to be extremely well rinsed, and afterwards the chiller needs to be sanitized with a sanitizing solution. If you have a pump, an effective way to sanitize a counterflow chiller is to circulate 170F+ water through it from the hot liquor tank for 5 or 10 minutes.