Use a terry towel and lay the applique facing the towel, pressing from the backside. Use a little steam. This will prevent the applique from flattening.
Do we know the difference between ironing and pressing? Ironing is the old fashioned rubbing back and forth. Pressing is to set the iron down, no scrubbing; lift the iron and placing it down again. No scrubbing. Therefore, no distortion.
Suzanne