The prefix se- means "apart", so when you segregate something you set it apart from the herd. The word typically means separating something undesirable from the healthy majority. During the apple harvest, damaged fruit is segregated from the main crop and used for cider. In prisons, hardened criminals are segregated from youthful offenders. Lepers used to be segregated from the general population because they were thought to be highly infectious. The opposite of segregate is often integrate, and the two words were in the news almost daily for decades as African-Americans struggled to be admitted into all-white schools and neighborhoods.