Hi Mohit,
You have to take form 26A from your employees and it has to be certified by CA, then submit it to your local AO where your TAN has jurisdiction.
The provision of Form 26A are given as below.
In Budget 2012 CBDT has introduced a provision w.e.f. 01.07.2012 by which a person who has defaulted in payment of TDS / TCS will not be deemed to be a person in default if he furnishes a certificate from CA to the effect that the person in respect of whom default is committed
(i) has furnished his return of income under section 139;
(ii) has taken into account such sum for computing income in such return of income; and
(iii) has paid the tax due on the income declared by him in such return of income,
and the person furnishes a certificate to this effect from an accountant in such form as may be prescribed:]
The above was done by inserting proviso to sub-section (1) of section 201 & to sub-section (6A) of section 206C. The CBDT has now issued the format of such certificates (Form 26 A for default in Payment of TDS & Form No. 27BA for default in Payment of TCS) and issued a notification related to same which is as follows :-