Change shoes. Unfortunately high heels do a number of things to our feet to cause pain and they can and do contribute to deformities from long term use. The best way to avoid these problems-don't wear them or at the very least limit the time you spend wearing them.
More information. More information is needed, such as where the pain is, when does it occur, how long does it last.
Have it evaluated. Wearing high heels can cause abnormal pressure distribution to your forefoot leading to potential problems. Shoes with improper support may be one cause of your foot pain. Try wearing a properly fitting shoe with a good arch support.