I worked for a company that paid me Per Diem in 2008-2009. They did not include it in the W2 as I guess it was from their Accountable Plan. By looking at the rules figured out that I should have not been eligible for Per Diem. As I was not commuting to work location, rather I moved my residence to the new location.

How do I correct this situation. Can I file amended returns treating it as a 1099-MISC, even though I did not get a 1099-MISC

So you got paid per diem and was NOT taxed on the per diem payments, and you wish to amend your return to claim the per diem as taxable income.

You can amend the return and claim the per diem on Line #21 of Form 1040. That way, the money will not be subject to self-employment tax.

However, I suggest you contact your payroll to determine WHY they did not tax it. You might find their explanation in probably in accordance with current tax law.