She probably just used her passport. Ok. You will need to apply for her to get a new Residency status through you.
You will need to file an adjustment package. This includes the following forms: I-130 (Petition for family member), I-485 (application for Lawful Permanent Residency), I-765 (Application for work permit), I-131 (Application for Advance Parole - but do NOT apply for this with 180 days or more of being illegally in the U.S.), G-325a (Biographic data - one for each of you), I-693 (Medical exam that a certified doctor must fill), and I-864 (Affidavit of support). You will need to file each form with supporting evidence and appropriate filing fees. You can find these forms at www.uscis.gov/forms.
The supporting evidence that you would file would be birth certificates, proof of your U.S. Citizenship, proof of her legal entry into the U.S. (in her case, that is just including a copy of her Canadian passport), and financial documents of yours to prove your income over the last year at least.
In about 3 to 5 months after filing, she should get a work permit. About 5 to 7 months after filing you should get an interview. If all goes well, a few weeks later she should get a Residency status (green card).
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