When exporting a contour plot, surface plot, or other 3D graph to a WMF or EMF format, a black box sometimes appears around the graph or instead of the graph. This is due to the fact that the contour, surface, and 3D graph types are bitmaps in Grapher. When exporting a bitmap to a metafile format, multiple "layers" are exported. One of these layers appears as a solid black box when the metafile is broken apart. This can also happen when the file is printed to some printers or copy/pasted into some programs.
To correct the issue when exporting the file, click the File | Export command and export to a different file format, such as TIF, PNG, JPG, BMP, or PDF (Raster). These are the preferred export formats for exporting of 3D graphs.
To correct the issue when copy/pasting the file, choose Paste Special in the other program. Select to paste as a Device Independent Bitmap. This is the preferred paste format for pasting 3D graphs.
Updated September 29, 2016