Not sure exactly what you mean by *lines*. However, if you start with a box object (it has 6 faces), calling the make hole function is going to make a hole in each face. If the box is being used it probably has 4 *thin* faces ... could these holes be your lines?
If you only want a hole in one face ... highlight it by switching to vertex mode then selectiong the vertices for the face you want to make the hole in. Now select the make hole function. A hole in only one face.
Regards,
griff