You have posted that, you have submitted resignation. It is believed that you have not submitted notice of resignation. Since your notice period accepted by you is of 3 months you have to tender notice pay for the shortfall in notice period.
You can submit a gentle letter, under acknowledgment, addressed to good offices of your appointing authority, MD/CEO, Head-HR, and ask them to supply you, by registered/speed post, acknowledgment and acceptance of your resignation, to adjust notice pay @ basic pay ,in your FNF statement, against amounts payable to you, FNF statement, payment of your dues payable to you, work experience certificate/service certificate, form 16, PF accumulation reports/withdrawal-transfer forms, NDC, relieving letter, etc. You can prepare your own statement of amounts payable by you to company and amounts payable to you by the company. You can mention that as per FNF statement if any amount is payable by you, it may be informed to you in writing, so that you can supply it by cheque payable to company against acknowledgment.
You should submit the company property if any with you, and ask the company to whom you should submit company property, and an appointment may be fixed with the designated employee and designated employee may be asked to issue the acknowledgment on the spot to you. It is believed that you have completed all tasks/assignment on hand and you enjoy good rapport with your reporting authority, and you have not signed any agreement/bond with the company.
In case there are no differences company may issue relieving letter. Company can sit on relieving letter.
The FNF statement, acknowledgment of company property and no dues remarks on the same can be accepted as sufficient by your current employer.