A manifold assembly that directs fluid to and from individually selectable sample receiving trays of a tissue processing system includes a manifold, fluid conduits machined in the manifold, and valves that may be selectively configured to provide a direct fluid path to or from a particular tray. The valves are controlled by a controller that positions each valve such that a desired path is created. Pressure is created in supply and/or drain bottles to supply or drain fluid from the trays supported by the manifold assembly. Independently operated heaters are provided on the manifold assembly to heat the trays to desired temperatures. Thermoelectric cooling elements may also provided to cool the heaters and/or trays.