Search for a filename with keyword
os.walk gives you the filenames already. There is no need to use glob to get them from the OS again. The looping could be done like this:

for path, dirs, filenames in os.walk(usePATH):
    for f in filenames:
        if f.endswith('COMPARE.mat'):
            ...

Updating a GUI can be slow. While I'm not familiar with what you are using, I would try if eliminating update_idletasks from the inner loop speeds it up.