Methods of priming a plasma processing system are disclosed. The plasma processing system has a number of different fluid flow circuits that are defined by sources of fluid, fluid flow paths, waste containers, a mixer, a separator, valves and a pump. A first fluid circuit is flushed, where the first fluid circuit is defined by a source of a first fluid, a first valve positioned between the source of the first fluid and the first fluid flow path, a second valve positioned between the first fluid flow path and the second fluid flow path, a first pump positioned between the second fluid flow path and the third fluid flow path, and a first waste container in fluid communication with the third fluid flow path. A second fluid circuit is then flushed by closing and opening certain valves.
