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Help > Using the Automated Tools > Automatic Referencing > Automatic Referencing Dialog > Stages of Automatic Referencing > Which Objects? 
Which Objects? 

Decide whether to reference all Marked Points in the project, or just those in the selected layer:

        Some projects are naturally one sided and so all items in the project can be successfully referenced together.  If you have a more complex object or you wish to reference only a subset of the items, you would place a subset of points in a Layer (see Layer Dialog) and then use the "All points in layer:" option (the same goes for silhouettes if the silhouette option is selected). Note, because some points or silhouettes are not yet referenced, you will have to place all marks on all photographs, which are part of this subset, into the same layer. You can segment an object this way into multiple parts by using multiple layers and then run automatic referencing on them separately.  Layers are saved with the PMR file so you can repeat the segmenting and processing as needed.