In our facility you have two ways of sorting cells: using a flow cytometry based sorter (BD Aria or FacsMelody) or a magnetic separation based one (Miltenyi autoMACS). The Aria and Melody works as the other Flow Cytometers to identify the population of interest, then the stream hits a very fast vibrating nozzle. Moving through the nozzle breaks the stream into tiny droplets. These droplets are electrically charged up, then the droplets with cells trapped in them can be diverted into collection tubes. The Aria is excellent in finding and separating the population of choice, regardless if it is labeled on cell surface or is distinguished by fluorescent protein expression. However, this method sorts cells one after another and particularly if only a low percent of your population is of interest it may take long time to get large numbers. Also, the machine costs over $400,000. In contrast the autoMACS uses magnets to pull out cells that are labeled with magnetic bead coupled antibody (or the opposite, the unlabeled cells). This allows processing tens of millions of cells in a matter of tens of minutes at a relatively low cost. The autoMACS, however, cannot sort intracellular GFP expressing cells and there is lot less control over the sub populations that you may want to sort.
Both sorters can be run aseptically, i.e. relatively germ free. Taking the right percussions with minimal luck you can keep the cells that come out of the procedures in culture without contamination.