Poorly asked question. Do you get 2 new X and Y matrices by regular intervals, or is time-dependency something represented by the index of X and Y? Does the Matrices then grow, or are they static. what do you want to save into a new variable, and should this be in memory or as a file.
In general, no matter what your specific problem is, especially with time-varying, multi-dim data, Matlab can be tricky to use. May I recommend you check out this submission, as it may hold your answers: