This is how I go about cleaning the General Hydroponic's Aero Flo 60 that I run. I know not all systems are the same, but this should give you an idea. When I get done with a run and get ready for the next go I clean it to look like brand new. Here it is plants chopped net cups with hydroton still there.
I start with three empty buckets one for roots, one for hydroton(yes I reclaim), and one for the net cups. Notice on the first orange bucket there is a serrated knife. I lift the net cups and use that knife to saw off the roots flush with the bottom of the cup. dump the hydroton in one bucket and net cups in the other.
Once that row is all cut off I pull the roots outta the end. They almost always come up in one matted heap.
Once all the roots are puled I fill the rez with 25 gallon of warm to hot water and a half gallon of bleach and run for an hour and sometimes overnite(just depends on time and schedule. This machine has risers to adjust the nute level in the tubes I lift them all the way up so the cleaning solution runs along the sides of the tubes.
After a good flush. I start the tear down. I take each tube one at a time and lay em across my washer/dryer. And here are some of the tools of the trade. Bleach, dish soap, scrub brushes. The toilet brush is curved and work well for scrubbing the inside of the tubes. I also have a sponge with scratchpad that is attached to a refillable handle that I put dish soap in.
With the risers still all the way up, fill again with hot water a lil bleach and dish soap and scrub the inside with the brushes. I use this water to also clean the outside. The tool you see below is called a 5 in 1 tool(or painters tool) found in the paint dept. There gets to be quite a bit of salt build up around the edges of the net cups and this works great for scraping it loose. You could use a single edge razor blade as well.
Next I pull the feeder lines. This is a step most home made systems won't be able to do. Anyways I pull the nutrient feeder line, there is a cap at to end I pull 2nd pic shows this. Then I just hook it up to the hot water line and run hat water through it and flush real good. Then I replace the cap and at low pressure run more hot water to make sure the laser drilled holes are free of all salts build-up.
Then repeat till the tubes are all clean. Then scrub out the rez. And it's ready for reassembly..