。
She thought I was a special friend of hers.
Literal
She [topic-は] my special friend [as-だと] was-thinking.
The Xを Yだと思う ('think of X as Y') frame, here without an explicit を — the implicit object is 私 ('me'), inferable from context. The progressive 思っていた ('was thinking, had been thinking') marks a sustained past mental state rather than a one-off realization, suggesting the belief was held for some time. 特別な ('special') is a な-adjective; the な before 友人 is the standard adjectival linker.