Convert the 3D N-by-M-by-Z matrix into a 2D Z-by-(N*M) matrix and use unique with the rows option on that. An example:
M3D = cat(3, [1 1 ; 1 1], [1 1; 1 1], [2 2 ; 2 2], [1 1 ; 1 1])
M2D = reshape(M3D, [], size(M3D, 3)).'
[~, i] = unique(M2D, 'rows') ;
Mun3D = M3D(:,:,i)
% which you can also do in an incomprehensible one-liner ;-)
% Mun3D = reshape(transpose(unique(transpose(reshape(M3D, ..)) , ..)), ..)