This setting defines the design files that will be selected by the pen table for processing. You can select the active file and any references by their slot numbers. References also can be selected by their logical names.
Using logical names for references produces more reusable pen tables. For example, you may have a number of design drawing files that use the same references, including the border file, but in different slot numbers. Selecting by logical names ensures that the correct resymbolization occurs for the references, irrespective of their slot numbers.
To identify the master file, you need to use its slot number, which is always zero because it does not have a logical name.