word-forming element meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant, a tendency which began in later Latin), from Latin in- "not," cognate with Greek an-, Old English un-, all from PIE root *ne- "not."
In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.
early 15c., separaten, transitive, "remove, detach completely; divide (something), sever the connection or association of," from Latin separatus, past participle of separare "to pull apart," from se- "apart" (see secret (n.)) + parare "make ready, prepare" (from PIE root *pere- (1) "to produce, procure"). Sever (q.v.) is a doublet, via French. Intransitive sense of "to part, be or become disunited or disconnected" is by 1630s of things, 1680s of persons. Related: Separated; separating.