Plot data (3d) only inside polygon

I am trying to plot data (45*56*6) only inside polygon and i tried these steps

imported shapefile and run query to sperate data point inside and outside polygon as

for i=1:6;
isin = inpolygon(X,Y,S.X,S.Y);
test(:,:,i(~isin)) =  NaN;
end;

and plot

for i =1:6
    subplot(3,2,i);
    imagesc(D_masked(:,:,i));
    set(a,'AlphaData',~isnan(a))
 end

but it did not work for me as

 imagesc(xyz,'AlphaData',~isnan(xyz))

xyz here is equal to 45*56 2d data.

Any kind of help is appreciatable.

[KSSV]

It can be done...what problem you are facing? Don't use imagesc. Use pcolor.

[Shakir Hussain]

In first section crossponding values of each slice of 3d data with logical 2d data has to replace with NaN by keeping rest of all values as it is (that are 0-100) which I could not figure out. Secondly I would like to use imagesc instead of pcolor.