Of course it can.
It would require learning MATLAB. It would require a clear understanding of what you are comparing, and what subtle variations will happen in some of those invoices. Making a computer do this automatically is often a complex task, and it will often make mistakes or just fail when something unusual happens. Will something unusual happen? OF COURSE IT WILL!
Can we help? Not really. It will just require painstakingly written code, depending on the complexity of what you will need to compare, knowing what compares to what. Sorry, but this sort of thing is something that you can do well, and a computer has a tough time with. If it was easy, then why do you say that it can take hours to wade through?
I would suggest that you write down the complete specs for what these invoices contain. Then you will know how to read them into MATLAB, and what you will need to compare. You need to know a clear algorithm for what you are comparing. Once you have all that, as well as a sufficient working knowledge of MATLAB, then the code will be easy to write. The better job you do of documenting what problem you need to solve, the better job you will have of ever writing the code.
Will you be writing said code? If it is you, then you need to learn MATLAB. If you are doing it, then you need to understand that you build a complex system one piece at a time, especially if you have not even a clue about how to use MATLAB. Of course, in that case you will gain by finding someone who is capable of writing that code for you. In that case, there is no rel reason to think that MATLAB will do a better job than code written in some other language. In fact there you will gain by finding someone who is competent in SOME language, and not worrying about the specific language. Instead, you want someone with the requisite programming skills, someone who you are able to work with. Then you will need to work with them to teach them the task they need to solve.
A virtue of code you will write yourself is then you will understand it, and understand how to deal with the inevitable problems that arise. A disadvantage is then you are the person who will need to be there to fix those problems, as the owner of the code. An advantage of someone else writing the code is you will get more professionally written code. A disadvantage of someone else writing it, is after they are gone, you still own it, and there will be inevitable problems.
Finally, a sad thing is that even when you do a perfect job of this, next week, next month, or maybe next year, the invoice format will change, because it is under the control of someone else, and they don't give a hoot about your problems.
