| For 2006, you should NOT have paid Social Security and Medicare taxs while on OPT.
First, ask your employer to refund these withheld taxs. It may not be too late. If not, get the employer's refusal in writing, as you will need it when you file Form 843. The filing of the Form 843 is totally separate from your federal income tax return. There is ONE LINK, however: You MUST file as a non-resident alien in 2006 if you want to get these withheld taxes back.
Now, since you are Canadian, your U.S.-based salary may be liable for Canadian taxes. I do not know for sure, but a call to a Canadian tax professional should get you an answer. | 
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