Hi Antonio,
I downloaded your notebook, but I'm not entirely sure I understand the problem... Does one of these things help you? Also, please take a look at the Documentation for Part and Flatten for more examples.
test = {{1, 2}}
test[[1]]
(*returns {1,2} *)
test2 = {{1, 2}, {3, 4}}
Flatten[test2]
(*returns {1, 2, 3, 4} *)
test3 = {{{1, 2}}, {{3, 4}}}
Flatten[test3, 1]
test3[[All, 1]]
(*both return {{1, 2}, {3, 4}} *)
Flatten[test3]
(*returns {1, 2, 3, 4} *)
