You can color, mark, exclude, hide, and label points that correspond to rows in the associated data table. You must select the points before selecting this option. See Select a Rectangular Area of Points and Select an Irregular-Shaped Area of Points in the Using JMP book.
To customize properties such as the marker size, text size, and grid lines, right-click the 3D scatterplot and select Settings. The Settings window appears. As you modify the settings, a preview appears on the 3D scatterplot.