Yes,while applying for the counselling you have to pay non-refundable registration fee and refundable tuition fee in online mode only through credit/debit cards and net banking.Given below is the refundable tuition fee and non-refundable registration fee 

NEET MDS Counselling Fees
Non-Refundable Registration Fees

For 50% AIQ/Central Universities Fee (INR)
General  : 1,000
SC/ST/OBC : 500

For Deemed Universities Fee (INR)
All categories : 5,000

Refundable Tuition Fees
For 50% AIQ/Central Universities Fee (INR)
General:  25,000
SC/ST/OBC:  10,000

Deemed Universities Fee (INR)
All categories : 2,00,000

A printout must be taken of the registration slip which will be useful for the further admission process which will be displayed on the screen after completion of admission process.