Mohammed - try something like the following. If mtx is your matrix
% create a 5x5 matrix
mtx = [-999 1 2 3 4;
5 -999 6 7 8;
9 10 -999 11 12;
13 14 15 -999 16;
17 18 19 20 -999];
% set all elements that are -999 to zero
mtx(mtx==-999) = 0;
This works only if the value you wish to replace is an integer.
Try the above and see what happens!
