If its not a problem with fit of your shoes, and they hurt even when you havent been wearing shoes, talk to your Doctor and ask him if it could be plantar fascitis. Plantar fascitis is swelling of the bottom of the foot..usually the thick tissues of the heel. It causes pain in the heel that tends to be worse in the morning and eases as the day goes by. It can also be worse after long periods of walking or standing, and is eased up with rest. Use an anti- inflammatory medication, ask your doctor about proper heel stretching exercises, and a night splint. Also get a good gel heel insert to help cushion your heels when youre standing and walking. Plantar fascitis takes a LONG time to heal.. Can be months until you have any relief, but keep with the heel stretches and anti-inflammatory meds.. It will get better. I had plantar fascitis when I was in my 20's, and it took quite a while to go away. I recently started having problems with it again, and am doing heel stretches every day. Good Luck.
It may be due to the type of shoe that you are wearing. I can't get over how I once bought running shoes, and to this day, can't wear them as after walking for a bit, they hurt. Sure felt comfortable in the store. Too bad they don't let you have a few days to test them out. Make sure you buy shoes at the end of the day, as this is when feet are most swollen and will be more comfortable. If you buy early in the day, as you wear, feet will swell and shoes will pinch and so on. Best of luck