Is there any possible way to make them of equal size ?
Possibly. As you haven't told us anything about what you want to do with them or why you want them the same size, we can't answer. You could just tack some constant number at the end of the shortest one (0 or NaN, probably), you could interpolate the shortest one (but how you define the interpolation again depends on why you want to match the size) or you could fix the bug that create a vector of an incorrect size if that's the problem.
By the way, it doesn't sound that you have mat files (files with .mat extension on disk which don't have mxn size). What you are describing sounds like vectors.
