Beginners do this sort of thing. They are tentative, almost afraid to use MATLAB, even when they think they need to. So they leave their data in files. Break your problem, ANY problem too large for you to figure it out, break it into small subproblems.
Problem 1: READ IN YOUR DATA. Bring in each file into MATLAB. Until you do this, you will constantly need to be accessing each file, dealing with the names of the files, etc. If the varius files have the same number of rows, then put it all into one 3-dimensional array. If they have different numbers of rows, then put the data into a cell array. Since you will be doing something else afterwards with this data, surely you need to read it into MATLAB eventually. Do it immediately, the first thing you do.
Problem 2: Once your data is in MATLAB, now the test is simple. It will depend on how you store the data, but there are simple ways to perform the test that would take at most a few lines of code to do. You will use find in the end to determine the indices of the datasets that fit all of the necessary rules.
If the problems above are still too large, then break them down more deeply. Eat a programming elephant, even a small one, one byte at a time.