Cats generally dislike having topical medication applied. Many cats run away after topical medications are applied and often act as though they have been "violated". Cats are smart and after a few treatments, they will often wise up to "the process" of getting topical medications.
Here are some tips for applying topical medications to your cat. However you hold your cat for the treatment, do it often – not just at "treatment time". Don't let them associate a certain handling technique with the application of the medication.
It is easiest to have two people available when applying the medication. One to hold and one to apply the medication.
Make sure the medication is ready! Many applicators require a puncture to the tip in order to "open" the tube. Make sure you are ready to give the medication before you have your cat restrained.
Very gently and without making a big deal of it, part the hair and apply the medication. Don't get excited or nervous during the process and your cat won't mind at much.
Never yell at your cat during this process. If you do, he will be more scared next time.
Apply the medication centrally on their back just below their necks. The idea is to apply it in an area that they can't lick off. Many products can be toxic or taste bad when ingested.
Offer a treat after the treatment. For some cats, this will take their mind off the "treatment".
For more information, please read Applying Topical Medications to Cats.