remove empty cells in MATLAB

If you want to delete all the rows in your cell array where all cell are empty, you can use the follwing:

a = { 1, 2; 3, 4; [], []}
emptyCells = cellfun('isempty', a); 

a(all(emptyCells,2),:) = []

a = 
    [1]    [2]
    [3]    [4]

The reason it didn't work in your formulation is that if you index with an array, the output is reshaped to a vector (since there is no guarantee that entire rows or columns will be removed, and not simply individual elements somewhere).