Hello student, the last year's cut off for a medical seat in AFMC was 551. The cut off marks may increases or decrease depending upon the difficulty level of the exam, number of students appearing for the exam, etc. 

As you have scored 540 in NEET, there is a slightly less chance of getting admission in the AFMC. I would suggest to not lose hope and wait for the cut off mark list which will mostly be released by AFMC in the month of June. 

Good luck!