Ok, so this is not strictly a software thing, but since it's very much basic for getting proper results out of scanning-software here goes:
The first two attachments show a burn of a Taiyo Yuden CD-R in an ultra-ultra-slim (7mm) notebook burner. Somehow a rather huge 'fluff' of dust managed to get right on the middle of the surface while the disc was taken out of the notebook and transferred into a Plextor for scanning. As you can see it caused a huge spike of C2 errors. After removal of the dust the disc showed perfect results.
The second two attachments show a burn of a Verbatim 16x -R in a Plextor 760. This disc had a rather big fingerprint on the outside area and some additional dust bits for good measure. You can see this led to increased PIE and PIF values in the affected areas. The extra dust bits apparently causing the PIF mountains. After careful cleaning the error levels turned out visibly better in a second scan.
So if you want your scans to be meaningful in any way: Make sure your discs are as clean as possible!