Constructing 3D Pandas DataFrame

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First, I think you need to fill C to represent missing values

In [341]: max_len = max(len(sublist) for sublist in C)
In [344]: for sublist in C:
     ...:     sublist.extend([np.nan] * (max_len - len(sublist)))

In [345]: C
Out[345]: 
[[7, 11, 56, 45],
 [20, 21, 74, 12],
 [42, nan, nan, nan],
 [52, nan, nan, nan],
 [90, 213, 9, nan],
 [101, 34, 45, nan]]

Then, convert to a numpy array, transpose, and pass to the DataFrame constructor along with the columns.

In [288]: C = np.array(C)
In [289]: df = pd.DataFrame(data=C.T, columns=pd.MultiIndex.from_tuples(zip(A,B)))

In [349]: df
Out[349]: 
     one         two       three     
   start  end  start  end  start  end
0      7   20     42   52     90  101
1     11   21    NaN  NaN    213   34
2     56   74    NaN  NaN      9   45
3     45   12    NaN  NaN    NaN  NaN

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