Use logical indexing :
idx = A <= -5;
A(idx) = NaN;
where A is your matrix and NaN stands for Not a Number.
I advice you to read the getting started guide. In your case the second chapter is fundamental. More specifically the logical indexing part is http://www.mathworks.co.uk/help/techdoc/learn_matlab/f2-14896.html#f2-15124.