Yes, you have to pay the full Registration Fees of NEET UG All India Counseling if you want to apply for Deemed Universities (irrespective of the fact you want to join or not). The full registration fees (for participating in Deemed Universities) include - Rs. 500 Counselling Fee (Non Refundable) + Rs. 2,00,000 Security Fee (Refundable).

However, be assured that if you do not join any Private Medical College, the Security Fee will get refunded after the counselling gets over.

If you want to predict what all MBBS Colleges (including Private) you can get with your NEET UG Rank, you may use NEET UG College Predictor Tool - https://medicine.careers360.com/neet-college-predictor