Hint: It is more efficient to omit the find() in:
MOD_CER(find(MOD_CER==-9999))=NaN;
% ^^^^
If you remove some arbitrary elements from a matrix, the result cannot be a matrix anymore. A matrix needs the same number of rows for each column, and columns for each row. Therefore after
index_liq = find(MOD_CP == 2);
MOD_CER2 = cer(index_liq); % 668557x1 double
it is not clear, how you want to convert it to a matrix.
Look at this small example:
x = [1, 2; 3, 4]
x(3) = [];
Now this vector x with 3 elements cannot be reshaped or whatever to be a matrix.
If you want to keep the matrix form, you need something like this:
MOD_CER2 = cer;
MOD_CER2(MOD_CP == 2) = NaN;
