Hi,
if I understand correctly this should do the trick.
First I generate a matrix which is -hopefully- of the form you want to test my algorithm:
matrix = Table[Table[RandomInteger[8] + 1, {m, 1, RandomInteger[4] + 1}], {i, 1, 9}, {j, 1, 9}]
Then this function should do the trick:
Position[ArrayReshape[Length /@ Flatten[matrix, 1], {9, 9}], 1]
Cheers,
Marco
PS: You might also like
http://mathworld.wolfram.com/notebooks/RecreationalMath/Sudoku.nb
and
http://demonstrations.wolfram.com/SudokuGame/