This is a temp 90-day ban on non-reciprocating countries (and countries of concern), which the FBI said they are not able to properly vet (because those countries will not provide background info on the applicant, and some other reasons). It only affects non-citizens such as visitors, students, or employment visas holders - from leaving the country and coming back, and there seems to be a waiver process to help them.
They already have something like a 7 month backlog of applicants to process. 90 days is going to give them a chance to catch up and look for ways to improve the situation... Such as getting the "Implementing Uniform Screening Standards for All Immigration Programs" part of the order up and running.