Please elaborate your question. If it is a matter of optimizing the code, without the code is a little bit difficult, and what you want to do is unclear to me. Two general suggestions are: preallocate arrays before accessing them (matlab allows you to increase the size of an array but this requires that the software performs several operations that you can skip if you know the size of the array in advance); moreover, when doing a for for to visit the cells of a matrix proceed columns first and then rows, this is for the way matlab itself stores matrices in memory.