Why is my cat scratching his ears and crying, but they look clean?

It's probably an ear infection, often it cannot be seen from the outside. Ear infections are very common in dogs, it is usually caused by either yeast or bacterial disease. the treatment is usually simple and straightforward, you will have to take Lisa to the vet and get the ears checked, then a prescription ear drops will be prescribed according to the infectious agent.

Unfortunately some tests usually need to be run in order to attempt and find the cause of the scratching, the ears need to be inspected properly to rule out an ear infection, fleas also often cause this type of problem, and it could also be an allergy or some other skin parasites.

ANy abrupt change in behavior is a good reason to have your cat checked by your vet. Your vet and their staff are trained to gently but effectively restrain and treat your pet without undue stress. If he has something wrong with his ears, the condition could worsen and cause further complications if not seen to, such as ear mites, an infection, allergies causing itching, there are a number of possibilities. Your vet will give him an exam, concentrating on his ears, if there is any debris in them they will sample that for examination under the microscope and, based on these results, will be better able to tell you what is wrong and what the best treatment is for your cat.

I would definitely have his ears swabbed and have them look under the microscope for signs of an infection. Otherwise, this could be a sign of a neurological issue and he may need to see a specialist.

This is probably due to a severe allergy, although it could also be fleas or mites.

 First of all, in order to rule out skin parasites, high quality flea treatment is given. It sounded like your veterinarian has done it already. The next step is to treat the allergy symptomatically and try discovering the cause of the allergy.

 Food can be indeed one the most common cause of it. Some medications can be given by the vet in order to stop the chewing and repair the skin lesions (steroids and antibiotics usually). 

There is also a nice topical spray available, it's called Cortavance and you can get it at the vets.

 Hopefully you will see some results after all this, if not you and your vet should consider starting on a long term allergy treatment.

I am sorry to hear about your kitty! If her ears have been checked by a vet to ensure there is no infection I would be suspicious she could have an allergy, either to a food ingredient https://veterinarypartner.vin.com/default.aspx?pid=19239&id=4951526 (most often a protein source and not grain as so many pet food commercials would have you believe) or an allergy to something in the environment like pollen/dust/etc. https://veterinarypartner.vin.com/default.aspx?pid=19239&id=4952664 . I would recommend bringing Chessie into the vet for an examination. This often requires at least a short course of medication to get the itching under control, such as a steroid, Atopica (cyclosporine) or Apoquel. The vet can discuss if a diet trial with a hypoallergenic diet is recommended and help you decide on the best diet for Chessie to try.

Hi, thanks for using Petco Pet Education Center, formerly Petcoach! Poor Rey! From your pictures I think that Rey likely has an ear infection with either bacteria and/or yeast. Ear mites are also possible. Polyps can lead to ear infections are usually removed surgically. In order to diagnose an ear infection, ear mites or a polyp she needs to be examined by a Vet. They will provide ear cleaner and ear drops and if she has a polyp they can discuss surgical options. I hope this helps and I wish Rey the very best!