CD vs CD-R

In order to get electron microscopic photos of the recroded data on CD surface, the data has to be truely grooved on CD, meaning that they have to be pressed on CD. Data on CD-R does not work.
"A printed/pressed CD surface contains pits which represent the data. The pits can be read optically because they reflect light differently from the smooth surface. A CD-R has only a continuous groove filled with dye. When written, the dye changes colour, its reflective properties change, and it can be read optically just like the CD. But because the SEM shows only topography information, i.e. the shape of the surface, it would not see anything in the CD-R where only the colour of the dye has changed." - Antti J. Niskanen /Micronova/TKK

Structure of CD surface
quoted from USByte

A transparent polycarbonate (PC) polymeric substrate (layer) has the pits molded onto its surface. These pits are the coded data and carry the information. The areas in between the pits, which are 0.9 mm (microns) to 3.3 mm long, are called "lands". The substrate layer is covered with a thin reflective layer of metal (aluminum) and with a protective layer of lacquer. On top of the CD sits the label layer. 
Summarizing, the compact disk consists of:
• The label
• The protective layer
• The reflective layer
• The substrate layer.

A laser beam of approximately 780 nm wave length is focused on the data side of the disk into a spot of about 1 micron in diameter.  The laser moves in the radial direction over the fast spinning disk and scans the data track for the intensity of the reflected light.

For actual data encoding of a CD, please see
http://en.wikipedia.org/wiki/Red_Book_(audio_CD_standard)#Technical_details

Preparing CD

To prepare the CD for electron microscopic scanning, it has to be soaked the sample in approximately 10 weight-% solution of KOH (potassium hydroxide) which dissolves the aluminum (reflective layer. See the picture above). That also releases the lacquer layer (protective layer) on top. Finally the sample was coated with gold by sputtering.

Potassium hydroxide - Wikipedia, the free encyclopedia

Sputtering - Wikipedia, the free encyclopedia