And, once your iron is cleaned out, be sure to use only distilled water in it at all times. The brownish residue is mineral scale which built up inside your iron--from the dissolved minerals found in "hard" water. Distilled water doesn't contain any minerals at all--it contains nothing but pure h2o. You can buy distilled water at some grocery stores and most pharmacies--and it's pretty cheap, usually less than $1 for a one gallon jug.
If the CLR you are referring to is the Calcium, Rust, Lime Remover, I would run a diluted quart through your steam iron, and work it out on a sample piece of cloth, before you try it on your own clothes.