If you are talking about a shape layer then set the fill to none. Please study up on shape layers by type shape layers or animating shape layers in the search help field at the top right corner of AE and follow some of the community resources.
If you are wanting to make a transparent hole in a layer so you can see through the box then you can either use a mask or a shape layer as a track matte. Making a hole with a mask is achieved by setting the mask to subtract instead of add.
If you are just seeing the black background of the composition panel then you need to enable the transparency grid or put something below the layer with the box.
It's almost impossible to get anything done in After Effects if you don't take a fair amount of time to learn the basics.