you need to do a citric acid flush to your system. If you do a search on this forum, you will find the procedure. Its very easy and does a splendid job! - a DIY level of about medium is needed and you should understand how a cooling system flows so you can remove all the acid from the system.
however there is a caveat.
if your cooling system is very poor and is held together by rust only then the cleaning will uncover all the holes in it which can be small pipes all the way to headgasket or heater core in dashboard.