Dear sanjeev,
If the net salary income of the employee crosses the maximum exempted tax ceiling (ex:Rs.200000), the employer shall issue TDS certificate. Even if the final tax liability of the employee is zero, the employer shall issue a zero TDS Form16.
The employer can generate zero TDS Form16 from the tdscpc website. In order to do this, the employer should have uploaded the relevant information of the particular employee (with zero TDS) in the tin-nsdl website.