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However, most of the boxes have very low or zero value and I don't need to show them. How can I make these boxes transparent? I just want to show the boxes with non-zero value.

For the above 3D plot I use a matrix M to store the value of each box (i,j,k) and use the following algorithm to plot:

indPatch=1:numel(M);

[F,V,C]=ind2patch(indPatch,M,'v'); %Call the function ind2patch in order to plot 3D cube with color

xlabel('y','fontsize',20);ylabel('x','fontsize',20); zlabel('z','fontsize',20); hold on;

set(get(gca,'xlabel'),'Position',[5 -50 30]); %set position of axis label

set(get(gca,'ylabel'),'Position',[5 50 -15]);

set(get(gca,'zlabel'),'Position',[64 190 -60]);

patch('Faces',F,'Vertices',V,'FaceColor','flat','CData',C,'EdgeColor','k','FaceAlpha',0.5);

axis equal; view(3); axis tight; axis vis3d; grid off;