As someone who has used the Expect module from time to time, I can highly recommend it for those cases where you want your Perl script to communicate with a process that is normally interactive only.

It does take some getting used to, though, because you have to take into account the possible responses that the called process (in this case MATLAB) could give you back.  For example, you might have to anticipate getting back a program prompt, or certain types of output.  To that end, I've found it helps to do a lot of testing with different input sets to make sure your Perl calling program is handling every outcome robustly.

One of the slick things about the Expect module is that it lets you use the Expect functionality without programming in Tk (which I've always preferred Perl over); sort of "best of both worlds" situation.