I don't clip Jack's ears unless we are going to a show, and usually I just "pinch" (well, not actually pinch, but hold) the ear closed so the scraggy looking bits stick out, and then I just clip them off. You can do it with scissors, but I would be extremely careful. If you could desensitize your horse to clippers, that would be your best bet.
But the hair in the ears protects the inside of the ear, so really, it's actually NOT beneficial to straight up clip the hair out of the ears entirely, it can do harm if flies and ticks and such and get lodged in the horses' ears.
Cinnamon Whiskey 11 y/o 15hh Chestnut AQHA mare, 2'6 Jumpers