。
She tidied up the papers on her desk.
Literal
She [topic-は] desk [possessive-の] top [possessive-の] documents [object-を] put-away.
Two stacked attributive-の constructions: 机の上の書類 = 'documents [located] on top of [the] desk.' Each の links a noun to the next, building up a layered noun phrase. 上 ('top, above') is a位置詞 (positional noun) — used with の to specify where something is. 片付ける ('to put away, tidy up, clear off') is the workhorse verb for putting things in order, broader than 整理する which leans toward sorting. Common collocations: おもちゃを片付ける ('put away toys'), 仕事を片付ける ('finish up work').