Loss factors are area dependent. When specifying a loss factor at a junction, the base area is of critical importance. By default AFT Arrow adheres to the following convention: whenever it makes sense physically, the base area is always the upstream pipe flow area. However, this can be modified by the user. In most junction Properties windows, the base area can be specified as the upstream pipe, downstream pipe, user specified area or diameter.

However, some junction types, especially those that allow three or more connecting pipes, specify loss factors based on each connecting pipe flow area, whether upstream or downstream. An example of this is a wye in which each of the connecting pipes has a different diameter. The idea of specifying a loss factor based on upstream flow area loses meaning because there may be more than one upstream pipe. In these cases the loss factor is referenced to the base area of the actual downstream pipe(s) where it connects to the junction. The types of junctions that do not always follow the upstream pipe area convention are Tee/Wye, Branch, Tank, Assigned Pressure, and Assigned Flow. Other exceptions are Valves and Relief Valves specified as exit valves, and Orifice specified as an exit.