This would be much easier if you worked with logical indices rather than subscripts, because then you could just use &, e.g.:
M = your matrix
X = M(:,1)>99 & M(:,2)<0 & isnan(M(:,3))
and you would have your answer already.
But now that you have subscript indices, you can use intersect on each of those index vectors:
X1 = [1,3,4,5];
X2 = [1,2,3,4,5];
X3 = [1,3,5];
intersect(X1,intersect(X2,X3))
You can see how this will get ungainly for more vectors, which is why using logical indexing is much preferred. Note that numbered variables are a sign that you are doing something wrong, and that you should re-think your approach.
