folders = dir('*') ;
N = length(folders) ;
filenames = cell([],1) ;
n = 0 ;
for i = 2:N
if isfolder(folders(i).name)
n = n+1 ;
filenames(n) = dir([folders(i).name,filesep,'*.txt']) ;
end
end
Now you have all the filenames, you can get what you want using that.
c = ismember({filename(1).name},{filenames(2).name})
