Company demanding me to pay amount and holding salary after resignation

You may go through the employment offer letter for the conditions of employment and make sure that you complied with the conditions on resignation. 

If you have followed the rules properly then you can issue a legal notice to the company demanding the relieving letter as well as the arrears of salary and full and final payment too.

Why you are leaving the company? If it is for taking up another employment, lack of proper relief could pose problems.

As per the offer letter it was 90 days. But before me some others also exited. And also while I submitted my resignation mail and while my top manager accepted it to HR they didn't informed me regarding this issue. Can anything be done with that 

You cannot take shelter under the practice of others.

You are required to comply with the employment offer letter terms and conditions which you failed to observe, but are blaming the management/company for your fault.

You may better pay the compernsation for the remaining notice period that you did not serve at the time of resignation and then approach the company for getting all the other benefits. 

But for some people company changed rules and for me another rule. Is that legal. And also while I asked my line manager and while I mailed they accepted for 30days relieving and now only they are making issue

You can take legal action against the grievances caused by them to you and for doing injustice to you.