I figured out how to resolve that problem when I realized the power of "eval()".
For anyone interested in doing something similar, here's the code I have now:
% list of all folders in FilterFunctions:
flist = getAllFiles('FilterFunctions');
% prepare result
filterlist = struct('Name',{},'Classname',{});
for i=1:numel(flist)
[~,filename,fileext]=fileparts(flist{i}); % get just the filename
if (exist(filename,'class') == 8) && (strcmp(fileext,'.m'))
try
if(isa(eval(filename),'Filter'))
filterlist(end+1) = struct( ...
'Name', eval([filename '.Name']), ...
'Classname',filename ...
);
end
catch % no problem - its eval
end
end
end