First off, the big error in your code is:
if polygons(:,:,u)==1
This will only be true when polygons(:,:,u) is all ones. Furthermore, I'm not sure what you were trying to achieve with this if.
A simple way to do what you want would be to use a temporary variable to store the page you're working on:
count = 20;
for u=1:count %don't need semicolon at the end. don't need increment when it is 1.
polygon = polygons(:,:,u); %temporary 2d variable
polygon(polygon == 1) = main01(polygon == 1); %as you wrote
polygons(:,:,u) = polygon; %update page with temporary
end
But actually, the operation you're doing is a simple logical AND, thus you can simplify the code with:
for u=1:count
polygons(:,:,u) = polygons(:,:, u) & main01;
end
If the operation you're trying to perform between polygons and main01 are actually more complex, I would change a few things. First, I would declare polygons and main01 as logical. That way you don't have to do the == 1 anymore.
Secondly, instead of storing the polygons as a 3d matrix, I would store them as a cell array of 2d matrix. If I rewrite my initial example that way:
count = 20;
%first two lines just convert existing variables. Better to declare them
%that way in the first place
polygons = arrayfun(@(u) logical(polygons(:,:,u), 1:count, 'uni', false); %polygons is a cell array of 2d logical matrices
main01 = logical(main01);
for u=1:count
polygons{u}(polygons{u}) = main01(polygons{u});
%or:
%polygons{u} = polygons{u} & main01;
end
