Find accepts a logical vector and returns all the indices containing 1.
The problem is you are giving find a scalar value so it's going to return an empty value when height(i) < 6 and 1 whenever height(i) >= 6
Did you consider not using find at all? Instead you can switch to logical indexing:
6kmtemp = nan(size(temperature));
atLeast6km = height >= 6;
6kmtemp(atLeast6km) = temperature(atLeast6km);
You should preallocate 6kmtemp to whatever value you want the "empty" cells to have, I used NaN but you can define your own constants according to what makes sense for you