。
She thought I was a doctor.
Literal
She [topic-は] me [object-を] doctor [as-だと] thought.
The pattern Xを Yだと思う ('think of X as Y') uses を for the person being judged and と for the content of the judgment, with the copula だ linking them. Same frame underlies 彼を犯人だと疑う ('suspect him of being the criminal') and 彼女を天才だと思う ('think of her as a genius'). Without the を~と construction, 彼女は私が医者だと思った would also work but emphasizes the embedded clause's subject; the を-marked version foregrounds the judgment-target.