Creating Holes Based on Cordinates

I am utilizing 3D slicer to eventually 3D print an abdominal wall based on a CT scan. I have a set of coordinates that indicate blood vessels which supply the underlying tissue at various locations. How does one create holes in the 3D image at the various coordinates I have listed in the table. For example, I have coordinates that will say 3 cm to the right on the X axis and 2 cm superior on the Y axis. This utilizes the belly button as the central point.