Well you're not constructing a file name at all, and of course you're not then using that file name in a call to save() at all, so it's not surprising that no variables get saved to a file. Please see the FAQ for sample code to do what you want:
You'll see you can call sprintf() inside the loop to create a filename, then use save
for i = 1 : 10
MS_Num = Num_MS(i);
Hexagon(sizeL,radius,MS_Num);
thisBaseFileName = sprintf('MS_Num%d.mat', MS_Num);
fullFileName = fullfile(pwd, thisBaseFileName);
save(fullFileName, 'var1', 'var2', 'var3'); % Whatever variables you want.
end
Replace 'var1', etc. with the names of whatever variables you want to save in the mat file.
