Not all browns invalidate a hefsek taharah, a moch dachuk, or a bedikah. Whenever you find brown on these cloths, you should have them evaluated by a rabbi rather than assuming they are invalid.
It is not only permitted, but halachically encouraged to clean yourself as thoroughly as possible before performing a hefsek taharah. The purpose of the hefsek taharah and moch dahuk is to establish that uterine bleeding has stopped. Cleaning beforehand is encouraged so that old blood in the vagina should not mislead us into thinking that bleeding continues.
Some women use a douche for this purpose. However, please consult with your doctor before doing this. It should only be done if you do not find that it causes any irritation. Make sure to exercise caution with tampons, following the instructions that accompany them about length of time in the body, since there is a serious illness that can result, chas veshalom, from disregarding the instructions.
Please note, however, that you may not clean yourself in this fashion after the hefsek taharah, prior to performing the bedikot of the seven clean days. These bedikot are intended to confirm that you have remained clean after the hefsek taharah and moch dachuk. Cleaning oneself internally is permitted during the clean days, but one should wait at least fifteen minutes between washing internally and doing a bedikah. Thorough internal cleaning such as douching should be avoided. A stain found on a tampon (or any item inserted internally), during the clean days or at any other time, would be treated like a stain on a bedikah.