If you're running low on memory and it's using virtual memory on the disk, you will get a lot of speedup from switching to Solid state drives. For example compiling a program used to take over 4 minutes with my hard drives and how with my SSD it takes about 30 seconds.
You could also get more RAM. I have 32 GB and an i7 CPU.
You might also want to look into GPU computing, which requires the Parallel Computing Toolbox - there's a MATLAB webinar on GPU computing you can probably find.
A 100 by 60 array is not huge. What is inside each cell? If it's just a matrix with "several rows", then that's not big at all. Unless "several" means like a million or so - then that would be getting up there.
