Easy Solution, Always Works
Put your chip in a 2.5 x 2.5 cardboard/mylar holder. The mylar is transparent in the scan and does note effect image quality. Once in the holder, the chip can be positioned so that it is aligned as best as possible and should not move around while positioning it on the scanner. Since the holder is square, the holder can be positioned in the top right hand corner of the scanner, against the sides, and still be aligned properly. Of course you can never align the chip 100%. I use a simple photo editing program to rotate the image to within a tenth of a degree accuracy for the Caribbean ChipGuide. Using this technique scanning images has become a science, rather than an art. Good luck.