Alma is calling for a physical separation between the righteous and the wicked. It is unclear why Alma calls for the righteous to "come ye out" rather than expulsing the wicked from their midst. Perhaps it is simply another way of saying the same thing. In any case, Alma is suggesting that those who do not repent will no longer have place in the church, however much they might currently claim it. The final concept of the removal of the wicked is that they will have their "names…blotted out, that the names of the wicked shall not be numbered among the names of the righteous."
This appears to refer to an actual event. In Alma 1 we learn:
Alma 1:24 For the hearts of many were hardened, and their names were blotted out, that they were remembered no more among the people of God. And also many withdrew themselves from among them.
This blotting out of names had occurred but four years before. The idea that the names were part of a heavenly record, as well as an earthly record, is likely based upon Psalms:
Ps. 69:25-8
25 Let their habitation be desolate; and let none dwell in their tents.
26 For they persecute him whom thou hast smitten; and they talk to the grief of those whom thou hast wounded.
27 Add iniquity unto their iniquity: and let them not come into thy righteousness.
28 Let them be blotted out of the book of the living, and not be written with the righteous.