If you originally did the correct install method of adding silver killcoils or some biocide and kept the loop closed then you will be in good shape and the cleaning will go pretty easy.
To start the process.
The first thing to do is gather all the things that you will need to do the clean out. In building the loop you should have a good idea of how much liquid you needed so ordering a similar amount will be easy.
You may also want to get a new silver coil if that's what you used or some new biocide if you used that or you can try something new.
If you used one or the other and you want to try the one you didn't use then you can do that, your choice. New tubing can also be a choice to get if you want to replace what you have.
Draining the liquid. If you had made provisions for a drain then this is where it will come in handy in getting the liquid out, just get an empty container to put the liquid in while draining. If you did not make provision for a drain then you will have to find a convenient place to either remove a tube from a fitting or cut the tubing in a low spot on the loop. It will be a lot harder to do this if there is no drain outlet and this would be a good time to add one.
Depending on how long you have had you custom loop and the blocks you can chose to inspect the inside of the blocks for any buildup or corrosion that would interfere with the flow of the liquid. Some blocks like a CPU block will come with an extra rubber gasket so that if you decide to take it apart to inspect the inside you can replace the gasket if needed.
If you do take it apart you will find that the copper plate inside will have rows of what looks like pins and these pins can be in a design to maximize the flow of liquid.
There can be some build up of particles from the liquid or some corrosion but regardless of what it is it needs to be removed so a soft nylon brush with some running water should clean it off.
If you have video card blocks and want to clean them out you can do the same thing as long as you have an extra gasket in case something happens to the one that's there you don't want to be stuck with a broken or torn gasket and not be able to put the block back together.
Cleaning out the radiators , reservoirs and tubing. Now that the liquid is drained from the loop you can go ahead and start cleaning the reservoirs , using tap water and soft cloths wipe as best you can the insides. The radiators will have to be drained as they will retain some liquid and some tap water run through them to flush. A lot of people will replace the tubing at this point instead of trying to clean it especially if dye has been used.
Once everything has been drained and cleaned you now want to take some distilled water and flush the radiators, tubing and reservoirs with it. Also take some Q-tips and wipe out the inside of the fittings.
Now that everything is rinsed and put back together you can refill the loop checking for leaks like you did when you originally built your loop. Don't forget the silver coils or biocide and if you found any corrosion anyplace inside your loop you may want to add some corrosive inhibitor or use a liquid that comes with it premixed.