。
She was disguised in men's clothes.
Literal
She [topic-は] men [genitive-の] clothes [object-を] wear-and was-disguising.
着て (te-form of 着る) links two co-occurring actions: wearing and being disguised. The te-form here is doing the work English handles with 'and' or with a participle ('dressed in...'). 変装する takes a する-verb noun 変装 ('disguise') — a Sino-Japanese compound that suru-verbs naturally. The past progressive 変装していた ('was disguised') describes an ongoing state at a past moment, not a momentary action.