Is it possible for illustrator (cs5 or later) to open/maintain original PDF layers?

The real issue here is that of editability of general PDF files in Adobe Illustrator.

The fact is that Adobe Illustrator is not, repeat not, repeat one more time not a general purpose editor of PDF files, popular beliefs and perceptions not withstanding. The only PDF files that can fully and properly be edited by Adobe Illustrator are PDF files that were originally saved from Adobe Illustrator using the save editability option when created and if the PDF file has not been subsequently modified by any other software. In that case and that case alone, Illustrator “opens” and allows editing of the PDF file but instead of using the PDF constructs, uses “private data” that Illustrator itself put into the file at creation time describing the original .ai Illustrator content, styles, layers, etc.

In all other cases, Illustrator attempts to open the PDF file and convert it into an Illustrator file, but since Illustrator's imaging model is a subset of the full PDF imaging model, you can expect possible content loss or modification, color space changes (Illustrator only supports either CMYK and gray or RGB in an Illustrator file), and text re-encoding. Note that in all cases, Illustrator never uses the fonts embedded in the PDF file, but in fact requires the fonts referenced in an Illustrator file (including PDF converted to Illustrator format)  to be installed on the system itself; thus font substitutions are possible. Layers from a non-Illustrator PDF file are not preserved upon opening such a file in Illustrator.

Thus, to address your particular scenario, unless the map you downloaded in PDF format from the usgs.gov website is a PDF saved from Adobe Illustrator using the save editability option, you cannot access the layers in Illustrator. Furthermore, ignoring the layers issue, you may find the rest of your editing PDF in Illustrator experience somewhat lacking.

          - Dov