I don't think anyone has mentioned the "Straighten" feature in Photoshop.

Click on the Tool that looks like a crooked box on top of an aligned box. This gives you a tool to draw a straight line across your scanned chip, centering the line (vertically) on elements of the chip design that should be horizontal, and the image will be aligned properly.

If you scan is really off (like upside down), you may end up with the aligned image straight, but inverted. Just use the "Image Rotate 180) function and you'll have what you want.

I use Photoshop "Elements", which is the cheaper version, still legal Adobe product. It does seem to offer the Save Selection feature that David mentioned, but I've never used it.

Photoshop Elements is under $100, and versions that are one or two levels earlier than the latest are often available on ebay for much less. I use version 10, which is dated 2011, and it works fine. I believe version 11 is the latest.