Whether your clean days remain valid depends on the color of brown that you found. Some browns can make a woman niddah; others do not.
If you saw only a light brown (the color of coffee with milk), with no hint of a reddish tint, you may continue counting. If the shade was darker, or at all reddish, please bring your cloth for evaluation. When you have the cloth evaluated, you can also ask if this is a shade you need ask about in the future.
If each of the spots on your underwear was clearly smaller than a gris (about the size of a US dime or Israeli shekel), they do not invalidate your clean days. If any spots were larger than a gris, and were a problematic color as described above, they should also be evaluated.
If you'd like to share your location with us, we'd be happy to try to make a referral to a local rav or yoetzet who could evaluate the cloth.
Please write back with any further questions.