The swelling and deswelling of a cross-linked polydimethylsiloxane (PDMS) pad adhered to a block copolymer (BCP) film during solvent vapor annealing (SVA) provides sufficient shear force to produce highly aligned domains over macroscopic dimensions in thin films. Here, we examine how far this alignment can propagate through the thickness of a BCP film to understand the limits for efficacy of the SVA-S (SVA with shear) process. Films of cylinder-forming polystyrene-blockpolyisoprene-block-polystyrene (SIS) ranging from 100 nm to more than 100 mu m are examined using the same processing conditions. The SIS surface in contact with the PDMS is always well-aligned, with Herman's orientation parameter (S) exceeding 0.9 as determined from AFM micrographs, but the bottom surface in contact with the silicon wafer is not aligned for the thickest films. The average orientation through the film thickness was determined by transmission small-angle X-ray scattering (SAXS), with S decreasing gradually with increasing thickness for SIS films thinner than 24 mu m, but S remains >0.8. S precipitously decreases for thicker films. A stop-etch-image approach allows the gradient in orientation through the thickness to be elucidated. The integration of this local orientation profile agrees with the average S obtained from SAXS. These results demonstrate the effective alignment of supported thick BCP films of order 10 mu m, which could be useful for BCP coatings for optical applications.