Please ensure that you make a backup before using this, and check that it is doing exactly what you want. I have not tested it, and you might need to make modifications.
Assuming that the top folder's name is stored as a string in the variable 'top_folder':
d = dir(top_folder);
fnames = {d.name};
% remove pseudo-folders . and ..
dotstart = cellfun(@(s) strcmp(s(1), '.'), fnames);
fnames(dotstart) = [];
maxlen = max(cellfun(@length, fnames));
% pad filenames on front with 'A'
fnames_padded = cellfun(@(s) char(padarray(double(s), [0 maxlen-length(s)], ...
double('A'), 'pre')), fnames, 'UniformOutput', false);
[~, sort_index] = sort(fnames_padded);
fnames_sorted = fnames(sort_index);
for f = 1:length(sort_index)
fname = fnames_sorted{i};
fout = sprintf('%03d', f);
fprintf('Moving %s\n to %s\n', fname, fout);
movefile(fullfile(top_folder, fname), fullfile(top_folder, fout));
end
