An improved transport carrier for use in a fluid filled microwave sterilization or pasteurization system includes patterned electrically conductive layers or carriers which extend over or under items to be sterilized or pasteurized and occlude 1 to 30% of the area in the direct path of microwave emissions to the items. When the patterned electrically conductive layers or cages are present, heating of the items to be sterilized or pasteurized is substantially more uniform compared to when there is nothing occluding or otherwise interrupting the direct pathway from the microwave emitters to the items. Enhanced automation is achieved for sterilization or pasteurization systems by configuring the preheating and cooling sections as loading and unloading sections. Furthermore, superior fluid temperature control between the loading, heating, and unloading sections is achieved using double gates or dividers between sections.
