At the time of registration students have to pay two kinds of fee .
For Deemed Universities
Non Refundable Registration fee :- Rs. 5000/-(same for all candidates)
Refundable Security amount:- Rs. 2,00,000/-
e.g Any candidate opting for Deemed University will have to pay Rs 5000/- Non Refundable fee +
Rs 2,00,000/- Refundable security amount at the time of at the time of Registration.
For (15% All India Quota)/ Central Universities (DU, AMU, BHU and Jamia Millia Islamia,
Delhi)/AFMS & ESI
Non Refundable Registration fee:- Rs. 1000/- for UR candidates & Rs. 500/- For SC/ ST/ OBC/ PH
candidates.
Refundable security amount:- Rs.10,000/- for UR candidates & Rs. 5,000/- for SC/ST/OBC/PH
e.g. any UR candidate opting for Central Universities/ AFMS/ ESI will pay Rs. 1000/-+ Rs. 10,000=
Rs. 11,000 at the time of registration.
Any SC/ST/OBC/PH candidate will pay Rs. 500 + Rs.5,000 = Rs. 5,500 at the time of registration.

You can refer this site for more information regarding counselling.. 

https://medicine.careers360.com/articles/neet-counselling