You are only asking about the plotting, so I assume you already know how to load your data. I use dlmread since that will read an ASCII-delimited file of numeric data into a matrix, which sounds like what you want to do.
How are you assigning this data to a variable? Is your loading of the data also occurring inside the for loop? I assume so. Otherwise, the loop would be unnecessary.
I'd probably do something like this:
filename = ["Moo_1.dat";"Moo_2.dat";"Moo_3.dat"];
...
for fnum = 1:length(filename)
Moo = dlmread(filename(fnum));
...
hold on
plot(Moo(:,3))
hold off
end
