Very simply the (I, J)th cell in the internal matrix becomes the (J, I)th and vice-versa.
A matrix may only be transposed if it is composed of square “sub-matrices” which may or may not contain multiple levels and/or blocks; see 10.2.4. In the case of a stacked matrix with multiple levels of individual square sub-matrices each sub-matrix is transposed locally such that I and J are the “local” row and column numbers.
Note that there is also a special case of matrix transposition whereby a matrix stacked by blocks (10.2.4) may be transposed “by block” rather than by cell. See 10.8.10.