The clipping facility in MATLAB is intended primarily for 2-D plots. Therefore, when you have a 3-D plot, it is handled as if it is a 2-D plot.
As a possible workaround you can try the following:
Suppose the equation of the slicing plane is A*x + B*y+ C*z = D for scalar A,B,C,D, then the boolean expression
d = find(A*x + B*y + C*z > D)
will produce an index vector into the x,y,z matrices (all assumed to be the same size).
The following subsequent commands
n = NaN;
x(d) = n(ones(size(d)));
y(d) = n(ones(size(d)));
z(d) = n(ones(size(d)));
will produce x,y,z matrices with NaN's on one side of the plane. Plotting the data will produce the desired plot.
Here is an example:
A = .1; B = -1; C = .3; D = .9; n = NaN; N = 200;
[x,y,z] = sphere(N);
d = find(A*x + B*y + C*z > D);
x(d) = n(ones(size(d)));
y(d) = n(ones(size(d)));
z(d) = n(ones(size(d)));
surf(x,y,z,'edgecolor','none')
hold on
[x,y,z] = sphere(N); x = x*.5; y = y*.5; z = z*.5;
d = find(A*x + B*y + C*z > D);
x(d) = n(ones(size(d)));
y(d) = n(ones(size(d)));
z(d) = n(ones(size(d)));
surf(x,y,z,'edgecolor','none')
hold off
Note that starting with MATLAB R2014b clipping of 3D plots is fully supported: "The Clipping property clips plotted objects to the six sides of the axes box defined by the axis limits." Please refer to http://www.mathworks.com/help/releases/R2014b/matlab/release-notes.html
