When designs are overlapped, there may be stitches that are hidden, which you would like to have removed. This process is automatically done when you save a file (controllable by preferences) but you may want to preview the results before saving. The Remove Hidden Stitches will run the process on those stitches so that you can evaluate the result. The result is temporary, however, so if you change anything on the design page, the stitches will return. This happens because changing a design will almost always regenerate its stitches.

For applique designs, you can use the applique tab on the color properties to tell the program that certain colors are applique steps. The position and material steps will not have their stitches removed, as it is considered likely that you will need those stitches. However, the applique material would naturally cover over other stitches, and the material fill is used in the removal of earlier stitching. This is controlled by the Preference “When Saving.”