How to delete/alphadata values of 3d data outside polygon without change the dimensions of data

We can delete the values of matrix outside polygon as

data = 12*17*6

x,y,S.X and S.Y are belongs to polygon

isin = inpolygon(X,Y,S.X,S.Y);
 data(~isin) = [ ]

but it changes the dimension of data from 3d to single column

Secondly we can also use alphadata for 2d data easily as

 imagesc(2ddata) 'AlphaData',~isin(2ddata))

1) How we can use the AlphaData for 3d data?

2) How we can delete values of 3d data outside polygon by keeping the data in same dimension