The LOC function will find the location of the elements that you are looking for. Then you can use regular assignment to replace the numbers. For example, to replace all values -99 with a missing value, do the following:
proc iml;
x = {1 -99 3 4,
5 6 -99 8};
idx = loc(x = -99); /* find location of elements */
x[idx] = .; /* replace those elements */