Loosely,
In Draw, it means to convert all Draw rendered effects to bitmaps before exporting for final output.
In PhotoPaint, it means converting all objects to the background by combining all objects with the background.
Things like transparency, shadows, lenses, and other effects do not always translate into Postscript (read PDF) very well. Flattening these items before going to output helps ensure that you don't have any unexpected surprises on your output. When CGS is printing it does very well at rendering these effects to your printer. PDF files have a tougher time and often show bounding boxes, unusual gradients and a host of other artifacts.
If you let us know the program you are using (Draw or PP) and what types of things are in the file we can advise you as to the proper method to achieve the best results.