I am working in US on L1 visa. My wife is on L2. She came to US in 2009 and stayed in US for 18 days and then returned back to India. She does not have an SSN. I have a child who never came to US.
How should I file the tax returns as married filing separately?

If you have completed SPT in 2009, you can file as married filing separately or married filing jointly.

On separate return, for spouse SSN, write N R A.

With joint return, attach W-7 (ITIN application) for your spouse. You will get standard deduction of $11,400 and exemptions ($3,650 each) for both of you. Your U.S. Tax Return: The U.S. Visas (http://taxipay.blogspot.com/2008/08/us-visas.html)