ImageReg Cropping Tool?

[SebagoLakeRanch]

I had the USDA office scan a few 1964 DOQ maps for me to do a ImageReg. There were some white backgrounds around the image from the scan I wanted to remove. I selected the area with the cropping tool, I re-processed the image, and they still show up on the map. What am I missing?

[SebagoLakeRanch]

I was messing with it and the area I highlighted remained, so I changed my area to highlight what I wanted to show, not what I didn't want to show. I got it now, but I'm still not sure what I did to make the cropped area "active." As you can see from the picture, even though I have an area selected, both cropped/non-cropped were showing.