I assume you are talking about antibody production in a GMP facility. Both processes are used because each is not 100% efficient, and there is a very very high standard of virus removal to produce something that will be injected into people. Each process removes virus by several logs, and you add up the logs for the total virus clearance. See page 5-6 and Table 2 of the link for more details. The nano-filtration is done later because the more rubbish (virus, cell debris, aggregates etc) there is, the slower the filtration and the more the filters will get clogged and need to be replaced.

http://people.clarkson.edu/~wwilcox/Design/purantib.pdf