The Flatten Image command merges all of the layers of the image into a single layer with no alpha channel. After the image is flattened, it has the same appearance it had before. The difference is that all of the image contents are in a single layer without transparency. If there are any areas which are transparent through all of the layers of the original image, the background color is visible.

This operation makes significant changes to the structure of the image. It is normally only necessary when you would like to save an image in a format which does not support levels or transparency (an alpha channel).