Missed filing tax return for ay 2009-2010

Hi
I am salaried employee, and TDS on salary is already deducted and paid to Govt. I missed filing of Income Tax Return for AY 2009-2010. As per calculation I am eligible for refund of around 2000 INR. 
I am confused with wordings of Section 139(1) and Section 271 F of Income Tax.
Can anyone please help me as to what is the implication i.e penalty if I file Income Tax return now.
What if I donot file Income Tax return of that year but have filed of AY 2010-1011.