Hello,

I am a international student.

“ I did not receive the 1099-MISC for 2006 from the company, because I returned to my country in July 2007. I only reported the W2-form. I think the company reported my tuition to 1099 MISC.”---> In general, as long as your ER paid you, an IC, more than $599.99 for services provided to his business during the year, 2006, your ER'll MUST have issued you a Form 1099-MISC by the last day in January of 2007 and mailed to the IRS with the Form 1096 (transmittal form) by the last day of February of 2007.So, you MUST have received the 1099-MISC from your ER by the end of Jan. of 2007.
“1) Can I apply the supply expanses as education deduction?”---->I am NOT sure what you mean. What supply expenses????? As long as you qualify, you can deduct your tuition and educational fees as your qualified educational expenses but not books, supplies, or room and board. Your qualified expenses DO NOT include amounts paid for your tuition and fees from Nontaxable scholarships. So I guess No.
“2) Should I contact the company to ask them to refile the 1099-MISC form?”---->As long your ER keeps the old copy of the 1099-MISC( they usually need to keep for three years, I guess) You can request duplicate copies of the 1099s from the company that paid you though they can charge you for that as well. All that a 1099 does is substantiate what you were paid. If they don’t have the copy, then You'll need to fill out Form 4506-T to request your income documents. The IRS can provide a transcript that includes data from information return, 1099-MISC;the IRS may be able to provide transcript information of your 1099-MISC for up to 10 years.
Please visit the IRS Website here; http://www.irs.gov/pub/irs-pdf/f4506t.pdf
“3) Do I have to pay the penalty, and interest?”--->I guess so. Even though the IRS does not allow efile services for the 2006 nonresident alien tax forms – Form 1040NR-EZ and Form 8843, you, as an F1 or J1 visa holder, could mail your return without 1099MISC Form and could file an amended return as soon as possible( As long as what information YOU filed was incorrect ) at that time, 2007. Not filing a federal tax return can be costly — whether you end up owing more or missing out on a refund. The IRS may also impose a wide range of civil and criminal sanctions on persons who fail to file returns. If you owe tax and your return was not filed by the due date, including extensions, you may be subject to the failure to file penalty, unless you have reasonable cause for not filing. If you did not pay your tax in full by the due date for the return, not including extensions of time to file, you also may be subject to the failure to pay penalty, unless you have reasonable cause for your failure to pay. Additionally, interest is charged on taxes not paid by the due date; even if you have an extension of time to file. Interest is also charged on penalties
Please visit the IRS Website here; What Will Happen If You Don't File Your Past Due Return or Contact the IRS

Thank you so much about your kind answer.

“When I contracted with the company, they did not say about that they reported 1099 MISC for my tuition. I asked several time about the tuition, but they did not explain at all. “I did not reported the 1099 MISC for 2006, but if I would like to report the 1099 MISC for 2006 this year, what kind of form do I need? I really want to try again.”---> Since you have received income reported by your employer on a Form 1099 MISC. This sometimes happens when you are treated by your employer as an independent contractor rather than as an employee. If you have been issued a Form 1099 MISC and an amount appears in box 7 of that form, you will need to file a 1040NR as said, rather than a 1040NR EZ. The income in box seven will be reported on line 13 of the 1040NR. Then you will need to file Form 1040NR( Form 8843) and Sch C for 2006. As said previously, you MAY request a copy of 1099MISC for 2006 from your ER or You need to contact the IRS for the copy.If they don’t have the copy, then You'll need to fill out Form 4506-T to request your income documents. The IRS can provide a transcript that includes data from information return, 1099-MISC;the IRS may be able to provide transcript information of your 1099-MISC for up to 10 years.
( In general , this is NOT your case; however, your scholarship NEEDS to be reported on 1099-MISC Box 3, and you report it as other income on your 1040NR 21.)
As a F1visa holder,a Non Resident Alien, when you work as an employee, your employer USUALLY issues you a Form W-2 for the income the employer paid you during the tax year. You are NOT subject to FICA taxes for the first five years as a F1 visa holder. Sometimes your ER issues Form 1099 MISC for the payments made to you. Usually Form 1099 MISC is paid to an employee working as an Indepenent Contractor or Consultant, who is working on a project temporarily with the Company. Since 'Indepenent Contractor' implies running your own business, and getting paid for your work, F1 OPT, you are recommeneded to get their payment reported on Form W-2 to meet the INS laws. But if you get paid Form 1099 MISC, you are by law required to report it to the IRS, by filing Schedule C / Sch C-EZ along with Form 1040NR and Form 8843.When you receive Form 1099 MISC, your taxes are not taken out, hence you will pay taxes around 15.3% when you file Form 1040NR and Schedule C to report your Form 1099 MISC Income. However, as a nonresident alien, you ARE not subject o Self-employment tax on your income as an IC.

I really appreciate your kind answer.