If the surface or mesh data has a NaN (not-a-number) in it, then the location of the NaN will be blank (just as NaNs in 2-d plots leave blanks). The example below illustrates using NaNs to make certain parts of a plot transparent.
%Generate a SURF plot with peaks data
z = peaks;
surf(z)
%Change peaks data so that a portion of that matix is made up of NaNs
m = z;
m(15:30,15:30) = nan;
%Plot the new matrix, m where the x and y information consisting of NaNs
%represents a hole in the SURF plot
figure;
surf(m)
As of MATLAB 6.0 (R12) you can use transparency to set a face to be transparent.
