'pre-separate' originates from Latin elements: the prefix 'prae' (from Latin) meaning 'before' and the verb 'separare' (Latin) meaning 'to separate, divide'.

'separate' comes from Latin 'separare' which passed into Old French as 'separer' and into Middle English (var. 'seperaten'), eventually becoming modern English 'separate'. The prefix 'pre-' comes from Latin 'prae' and entered English as the productive prefix 'pre-'. Together they form the compound meaning 'to separate before'.

Initially 'separare' meant 'to divide or sever'; over time 'separate' kept that general sense. As a compound, 'pre-separate' developed the specific meaning 'to separate in advance' (i.e., do the separating before a later event).