Problems opening pdf's in illustrator.

When I open a pdf in illustrator, I get many individual objects and numerous squares that contain lots of information (like they have been flattened or merged).  I would really like to get the objects that make up these flattened or merged areas.  Has anyone encountered this before and found a way to get at the other data?

They would have to save from Illustrator the .pdf with preserve illustrator editing capabilites, or else the file is optimized for .pdf and the layers are flatttened, raster effects & images embedded. Once the file is optimized for .pdf that information is gone.
If a .pdf preset such as smallest file size was used, then images are not only comprfessed, but converted to RGB.

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