You are making your code far too complicated for such a simple task. Keep it simple, something like this should work:
S = dir('*.aqa');
for k = 1:numel(S)
[~,file] = fileparts(S(k).name);
ReadAquaScat1000(file,'SINGLE');
end
And if you really want a list with all filenames, it is easy to put them into one cell array:
names = {S.name};
Also note that it is probably simpler to pass the path as well, rather than navigate to the directory and change the current directory:
D = '.'; % path string
S = dir(fullfile(D,'*.aqa'));
for k = 1:numel(S)
[~,file] = fileparts(S(k).name
P = fullfile(D,file);
ReadAquaScat1000(P,'SINGLE');
end
