Top-level entities are any line, art, text, or other object that is not a die station (group or block). If you want the Pandora software to include top-level entities, you need to edit the DefaultUser.properties file.
Exclude Top Level is a setting in the Pandora software that removes any objects in the die that are equal in size to the whole die. For example, if lines trace the outer edges of the die, Exclude Top Level omits those lines, and the size of your die is set only to the outer boundaries of the remaining die stations. If you set the substrate size of your dies by using such lines, turn off Exclude Top Level. When this setting is turned off, Pandora software uses the size of the die from your file, not from the die stations, so you must set the size of your die correctly in your CAD creation software.