When I first got the scanner, I too was a bit surprised by all the natural shadowing that was thrown around by the scanner's lamp. I tried many different settings in the EpsonScan software but nothing worked the way I would have liked. The shadowing is primarily caused by the reflection of light against the edge of the chip and the bright (white) surface of the interior of the lid. You would not get as many shadows if you were to line the inside of the lid with a colored construction paper for example. Personally, I prefer to scan the chips with the scanner's lid open, then I bring the image into Photoshop where I crop everything but the face of the chip (circle crop), add a "simulated" shadow for depth, trim away the transparent pixels, then I resize. I like the size to be around 300x300 pixels. You can email me anytime if you have questions... I'd be happy to explain in further detail if you need. Good luck!

Another tip I could offer is that I generally scan about 12 - 14 chips on a single scan (then of course, the opposite side as necessary). I then bring that image into Photoshop (with multiple chips) and circle crop each chip as necessary - rather than scan one chip at a time. Have fun!