You can file the returns based on the form-16 issued
Press Release No. 402/92/2009 - MC (11 of 2009), dated 11-5-2009
The Central Board of Direct Taxes have decided to defer the implementation of Notification No. 31/2009 dated 25-3-2009 amending or substituting Rules 30, 31, 31A and 31AA of the Income Tax Rules, 1962. The amended / substituted Rules will now come into effect on 1st July 2009 instead of 1st April 2009. Tax deductors / collectors may continue to deposit TDS / TCS tax and file TDS / TCS returns as per the pre-amended provisions in the interim period