I hold J-1 visa and am a researcher from China, and sign the tax treaty form.
I can file tax forms to get federal and state fax back. But there are social securtiy tax withheld and medicare tax withheld over 1000 USD in total. Do I need to pay that or can I get them back and how? Thank you so much.

BTW, for the form 1040NR-EZ, do I leave the line 3 and 4 and 5 just blank? And put wages to line 6? Thanks.

Every one on J1 is exempt from SS tax and Medicare tax for 2 years.
Researcher from China is exempt from federal income tax for 3 years. You will file nonresident tax return and Form 8833 to claim your exempt status.

About SS tax and Medicare tax, ask employer to refund you the taxes, and stop withholding during the second year. Finally you can file Form 843 for the refund. It is filed separately. Read: Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual