We may clean it to our nose's satisfaction, but your cat and his keen senses will still be able to smell it. Remember the cats sense of smell is ultra sensitive. Your male cat may smell a female cat in heat from blocks away. The scent may come wafting in through an air conditioning duct or fireplace vent. If you move to a home where another cat has already left a strong scent, your cat may mark over those areas.
Cats are territorial by nature and they identify their territory by scent.
The more you can socialize your cat as a kitten, the less likely this problem will occur in adulthood. Keep this in mind when moving with your cat, boarding him, taking him to the vet or groomer, bringing home new furniture, or bringing home a new friend. Try to make your cat feel as non-threatened as possible by using familiar scents. For example, before bringing in a new piece of furniture, rub it down with some of your cat's bedding or even your own bedding. If you have a veterinary appointment, take both cats even though only one will be treated.