Read this http://matlab.wikia.com/wiki/FAQ#How_can_I_create_variables_A1.2C_A2.2C....2CA10_in_a_loop.3F you will know that it's not a good idea to create such name variables, you can just use one cell array
for ii=1:2
sim('Simulink_Model'); % Output: X
out{ii} = X;
end