If you are using layered PDF input files:

• Ensure that you set the PDF 1.4-1.6 (Acrobat 5-7) box in the Normalize section of the refine process template to Leave as is.
  Layered input files should be trapped at the time of generating instead of refining.

• Version layers and colors are automatically determined and populated in the version plan. In order to have the correct layers and colors populated:
  • Ensure that the colors in the refined files are the correct separation colors to be used in final output.
  • Map input layers to other layers using the PDF Layer Selection button on the Start Process dialog box.
    The layer mapping in the PDF Layer Selection dialog box is saved in the job's Control folder in a mapping file (Layer_Mapping.LPV) and can be used in the refine process for the next input file, if it contains a similar layer structure. When you open the PDF Layer Selection dialog box, the mapping is already there.
    Note: You can also apply the layer mapping automatically to other input files, assuming they have a similar structure, without opening the PDF Layer Selection dialog box. To do so, select the Map PDF layers automatically (by mapping file) check box located under PDF Layer Mapping, in the Normalize section of the Refine process template.
  • Make sure that versioned pages are not used as input files. Pages that were previously refined as versioned pages are not yet supported as input files.

Tip: You can determine the layers in a refined PDF by selecting the refined PDF in the Pages view, and clicking File > Get Info. You can also go to the View menu and select Visible Columns to obtain the same information.