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.
"bore through, pierce, make a hole or holes in," late 15c. (implied in perforated), a back-formation from perforation or else from Latin perforatus, past participle of perforare "to bore through, pierce through," from per "through" (from PIE root *per- (1) "forward," hence "through") + forare "to pierce" (from PIE root *bhorh- "hole"). Related: Perforating.
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<a href="https://www.etymonline.com/word/imperforate">Etymology of imperforate by etymonline</a>
Harper, D. (n.d.). Etymology of imperforate. Online Etymology Dictionary. Retrieved $(datetime), from https://www.etymonline.com/word/imperforate