Calculate the salary for the days he has worked, i.e., 24 days. Take the notional salary for 90 days/three months. Deduct the salary payable for 24 days from the notional salary for three months and pay it.
Remember that even when there is a clause that the employee should serve 90 days' notice or pay salary in lieu of that notice, you are not expected to hold the salary for the days an employee worked. You can collect the notice pay, if the law allows, but you cannot hold the salary earned by an employee. Also, remember that an employee coming under the scope of the Industrial Disputes Act need not give you any notice while he leaves the company, whereas in order to terminate an employee, you have to give notice. Therefore, when demanding notice pay or recovering notice pay or adjusting the notice pay from the salary due, you should remember these things.