I'm not sure why you would get a 0x1 empty double column vector. You may need to post some code to help figure this piece out.
You can also try simply indexing the weights from the network:
IW = net.IW;
b1 = net.b;
LW = net.LW;
Note, many elements of the cell will likely be empty (excepting the bias weights), but you will have matrices of the weights in the non-empty cells.