"I have a set of matrices F1,F2,....,F16; ..."
Which is the problem -- do not create multiple variables with sequential names, create these as cell array in the beginning.
Then you can deal with them programmatically via cell2mat() or address each as needed.
Probably given the need to build the 2D array a 2D array would be better than just 1...N
You'll have to build the zeros() arrays as well or use sparse() array addressing modes.