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Set all the useless things aside.
Literal
Useful not-be things [topic-は] all separate [at-に] put-[keep-ておく][command-なさい].
別にしておく — 別 ('separate') + にする ('make into') gives 'set (something) apart,' then ~ておく ('keep in a state') gives 'keep set aside.' 全部 ('all') specifies the scope as 'all of them.' Note 役にたたない is the kana-only form of the same 役に立たない phrase.