Not all staining makes a woman niddah. For example, spotting found on colored undergarments does not make a woman niddah. For more information, please see our site's articles "Ketamim" and "Toilet Paper."
When staining does make a woman niddah, it is sometimes possible to achieve a hefsek taharah even before staining has totally ceased. A hefsek taharah and bedikah cloths need not be entirely clear, and any questions should be brought for halachic evaluation rather than presumed to invalidate the clean days.
When staining does not make a woman niddah, we usually recommend abstaining from relations for twenty-four hours as a precaution against the staining becoming a flow. Please note that this is a recommendation and not a strict halachic requirement.
At this stage, we do suggest consulting with your physician about your efforts to conceive and possible effects of your medication.
Please write back with any further questions.