Running parallel system Until System Completely Cleaned of virus.

I overheard an IT Pro who is installing new hardware and software at a client, that the client will have to run parallel systems until all the virus have been removed from the old system. The old systems is Windows NT network, Windows NT workstations,

Since I am only an accountant, I wondered if the IT guy knew what he was talking about.

Why can’t he just clean the server and workstations with AV software?