Here's what I've been doing lately:
Cut a circle around the stem and pull out as much as possible. Scrape those off onto a paper plate. Cut the chili in half and take out the rest. Try to keep just individual, healthy seeds. Fill a cup w/ 1 part bleach, 5 parts water, add the seeds and shake or stir vigorously. Strain and rinse the seeds. Let dry on a paper towel.
I recently took some seeds from dehydrated, halved, chilies. They ended up being very nice seeds and very clean. Taking dried halves and working the seeds out w/ a spoon might be even easier than above.