If I understand you question correctly, you want to get the intensity information of the second image, using coordinate values you extracted from the first image.
You should be able to do that, but you need to make sure that both pictures have the same coordinate "system". Specifically, you need to know that point (10,10) for example, is in the same location in both images.
In case you are using different cameras to get the pictures, or because of the different content (color image vs depth), there might be some registration issues (i.e. misalignment). There are some techniques that might allow you to register the two images so the coordinates will be similar. You can find more information on Image registration in the following documentation link:
Keep in mind that the two images are different (not having very similar features) and you might need to spent some time understanding what is the best registration method to use.
Assuming that the pictures are registered, once you have the coordinates from the first image, it is easy to make the rest of the values black for the second image.
Here is an example:
% Read a test image - This represents your second image
A = imread('TestImage.JPG');
% Assume this is the coordinates that you are interested in from the first image
X = 50:400;
Y = 50:200;
% Initialize the new image to zeros
New_image = zeros(size(A));
% Only copy the coordinates that you are interested in
New_image(X,Y,:) = A(X,Y,:);
% Show the image
imshow(uint8(New_image))
