If you read the video file frame-by-frame, then it is a simple matter of matrix-indexing to remove a specific area (make it black as you said):
for i=1:numFrames
% read next frame
frame = <.. get i-th frame..>;
% black out region
frame(100:200, 300:350) = 0;
end
If the frames are RBG, just adjust indexing appropriately: frame(a:b,c:d,:)=0