Converting the 3D Matrix to 2D Matrix

The general reordering of elements can be done by:

y = reshape(permute(reshape(x, Size1), Order2), Size3)

In your case (perhaps - still not sure what "i1, j1, k1 etc" means):

x = zeros(3,5,5);
x(:) = 1:3*5*5;   % Some test data
y = reshape(permute(reshape(x, 3, 25), [2, 1]), [25, 3])

If this is the wanted output, there is an abbreviation:

y = reshape(x, 3, 25).'

permute(Matrix, [2,1]) is the same as mtranspose() and the 2nd reshape is not required here. But it is worth to keep the general transformation in mind.