In some FieldTrip figures opacity is used to indicate statistical significance, for example in sourceplot where you can use color=functional-value, opacity=significance, grey-level=anatomy, or for example in topoplot.

You can use the Matlab command “print” for printing figures to a printer or for saving them to a bitmap or PostScript file (see help print). If you encounter difficulties printing/saving the figure, you should try printing with the extra option “-opengl”.