You would not be able to use a matrix, as matrices can only contain the same data types (all numerical or all character arrays) and must have rectangular dimensions (without empty spaces). You can't match up the columns of 'C3' and 'A2/C3', for example, because the latter has 5 characters (5 columns) while the first has 2. Use a cell array instead.
To get a column rather than a row from your output, transpose your b:
a='C3;A2/C3;C7;C9;A5/E1';
b=regexp(a,';','split')'
b will then become a 5x1 cell array.
-Nathan
