The first step you should do is to run your code in the Matlab Profiler. This will give you insight as to the specific bottleneck(s) in your code, and you can then focus your efforts to improve those.
For example, perhaps the main bottleneck is reading the disk file? or maybe parsing its data? or maybe the inner loop? Perhaps the loops run too many times than they should? perhaps you can calculate some loop computations outside the loop (rather than repeatedly within it)?
- All these are examples of questions that can only be answered once you have run your code in the Profiler and analyzed the reported results.