since you already created a binary mask you can just index multiply " .* " the mask with the original image as outside is 0 and inside the mask is 1.
%dummy image for example
img = imread('pears.png');
bwimg = single(rgb2gray(img));
[r c]=size(bwimg);
figure(1),subplot(131),imagesc(bwimg); colormap gray
title('original image')
%dummy mask gen for example
x = c*rand(1,4);
y = r*rand(1,4);
x(end+1) = x(1);
y(end+1) = y(1);
%create mask
bw = poly2mask(x,y,r,c);
subplot(132),imagesc(bw);colormap gray
title('mask')
%extractROI
%index multiply image with mask as outside is 0 and inside is 1
ROI=bwimg.*bw;
subplot(133),imagesc(ROI);colormap gray;title('Mask applied')
