At Angels of Assisi, we recommend and use ear tipping as a means to identify previously altered and veterinary treated feral cats. The reason for this is that feral cats may interact with a variety of caretakers, veterinarians, and animal control personnel during their lives. It is important that a universal method of identifying sterilized animals is used. Ear tipping is the only fully reliable method and is recognized internationally as it has been used for decades.
Notice that I called it ear tipping instead of ear notching. Tipping is preferred over notching, because notches may be confused with irregular ear patterns caused by fight wounds, frost-bite, and ear mites, whereas the tipped ear creates an unmistakable silhouette.
Ear tipping is performed painlessly under anesthesia and is much less invasive than the spay/neuter the cat is undergoing. It allows the identification of sterilized cats in the field so that they do not face the trauma of unnecessary transport and surgery again. It is the standard of practice accepted by animal welfare organizations and feral cat advocacy groups. The presence of a tipped ear does not appear to affect the adoptability of cats in the future. Tattoos and microchips may be used to identify individual cats, but neither of these methods can be read without handling the cat
When ear tipping, a straight hemostat is clamped across the top centimeter of the pinnae (about the tip 1⁄4 inch of their left ear) and the tip is removed by cutting straight across with a scalpel. The ear is tipped before surgery and the hemostat is left in place until the cat is returned to its trap. It is rarely necessary, but a styptic stick or cautery is used after the hemostat is removed if there is residual bleeding.
I understand your concern that ear tipping can be a painful and disfiguring procedure. However, consider that it is very traumatic for a feral cat to be retrapped and transported unnecessarily because of unclear markings. It is a major blunder to perform unnecessary surgery on a cat that is already spayed or neutered because it was not marked with a universally recognized symbol,. I have done this before.
Even worse would be the euthanasia of a sterilized feral cat because of uncertainty about the significance of a marking or the failure to notice a mark at all.
In addition we use pain medication pre-operative and postoperative by injection, meant to control pain for a spay which is a much more invasive and painful procedure than removing the upper tip of the ear. This is NOT the same procedure as an ear crop in a dog. Much more tissue is removed and a large amount of bleeding occurs during an ear crop. The vast majority of veterinarians will not perform ear croppings unless medically necessary. Most veterinarians will ear tip a feral cat without second thought. Cats wake up from their procedures without pawing or showing any signs of distress.
It is a very simple and easy procedure that we do often. I would encourage you to use it to identify your feral cats that have already been trapped. In my experience it rarely causes any problems and those problems have been minor and due to inexperience with the technique. It is safe. I have never seen an infection, a cat bleed excessively or an animal that seemed to be in pain due to the ear procedure. The only drawback is cosmetic.
Dr. Shelley Spangler, Information derived from The Association of Shelter Veterinarians