I have been using a golf ball to massage the muscles and ligaments in my feet, loosening them up. I press the sole of my foot down on the ball and move it up and down, from the ball towards the heel and back. At first, it was really painful, but now it falls into the category of "hurts so much it feels good." I've also been giving my feet massages, bending them in different directions.
Now my feet are flat on the ground in most postures that caused me trouble. I also noticed that my heels are much closer to the ground in Downward-Facing Dog posture, which may be due to looser hamstrings.

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