Replaces identified rows with zeros.
% Example data that match the indices in your question
M1 = rand(10,10); M1(:,2) = 1:10;
M2 = rand(10,10); M2(:,4) = [2:5,7:12];
M3 = rand(10,10); M3(:,10) = [1:5,7,9:12];
% Identify rows that should be eliminated; replace data with zeros.
idx = ~ismember(M1(:,2),M2(:,4)) | ~ismember(M1(:,2),M3(:,10));
M1(idx,:) = 0;
Note that row 6 should also be altered in addition to row 1 and 8.
If you'd rather delete those rows in M1 rather than replace the values with 0s,
M1(idx,:) = [];
