I am an international student (F1-vsia) coming to U.S in fall 2006. I worked on-campus as graduate assistant. I used Freetaxusa (FREE online tax preparation - 2008 income tax return filing | FreeTaxUSA.com) to file my income tax in April 2008. They used Form 1040 (federal tax) and Form SC 1040 (south carolina state tax) and it was accepted by IRS. The tax refund was deposited to my account later on. A few days ago, I checked my status, then found out I am not qualified as resident alien, so it seemed I filed the wrong form. I really want to know what I should do to make the amends.

On F1/OPT you are exempt from residency for 5-years. You must file non-resident tax return. Your income is not subject to FICA taxes.
You filed resident tax return for 2007, which was a mistake. You may file amended tax return Form 1040X along with properly done non-resident tax return and pay the tax due, if any.

Non resident tax return can not be efiled.
Read: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents