Polarity-switching photopatternable guidelines can be directly used to both orient and direct the self-assembly of block copolymers. We report the orientation and alignment of poly(styrene-block-4-trimethylsilylstyrene) (PS-b-PTMSS) with a domain periodicity, L0, of 44 nm on thin photopatternable grafting surface treatments (pGSTs) and cross-linkable surface treatments (pXSTs), containing acid-labile 4-tert-butoxystyrene monomer units. The surface treatment was exposed using electron beam lithography to create well-defined linear arrays of neutral and preferential regions. Directed self-assembly (DSA) of PS-b-PTMSS with much lower defectivity was observed on pXST than on pGST guidelines. The study of the effect of film thickness on photoacid diffusion by Fourier transform infrared spectroscopy and near-edge X-ray absorption fine structure spectroscopy suggested slower diffusion in thinner films, potentially enabling production of guidelines with sharper interfaces between the unexposed and exposed lines, and thus, the DSA of PS-b-PTMSS on thinner pXST guidelines resulted in better alignment control.