Since you don't provide more concrete details about your specific circumstances (code, examples, purpose, etc), I will give a fairly broad answer that hopefully points you in the right direction.
Feel free to respond back with more details if the below ideas miss the mark.
Consider using the Matlab "dir" function to scan for files, which you can have run recursively in newer versions of Matlab. Another newer feature you could use is the "datastore" approach. Type help for either dir or datastore and you should get some good info to help with what you need.