Liability paid in wrong head

Adesh if you meant you disclosed in GSTR 3B in IGST head instead of CGST+SGST, before proceeding to pay you can make changes in the 3B.

If not once proceeded to pay you would not be able to change the values in GSTR 3B. Payment must be made. 

Please see if you could be covered under Section 77 of CGST Act & 19 of IGST Act.

If not, based on Circular 26/2017 - reverse the tax positions in next subsequent GSTR 3B.

Where you do not have any tax liability in IGST head now, refund can be applied for separately.