We can't see what famplifire [sic.] is doing with your variables so there isn't any specific comments that can be made. However, the rule of thumb is basically that if you must loop through a small number of large arrays/matrices, it can be advantageous to hold them in cells. Otherwise, it is probably better to concatenate them into a single array.
Structures are essentially the same as cell arrays. They are just indexed differently.
