do you mean the invisible part is always invisible? in the sprite editor you can set the alpha channel to 0 and paint the part of the sprite you want to be transparent...
or do you mean you need to make part of a sprite that starts off visible suddenly become invisible?
you could do that with an animation, unless you need the invisible part to move across the sprite... then blend modes is what you need, like jobel said. (you can make a mask sprite that only blends with part of your source sprite).
if none of the above, then you will have to make an image to show us what you are trying to do.