Thermal scanning probe lithography (t-SPL) is applied to the fabrication of chemical guiding patterns for directed self-assembly (DSA) of block copolymers (BCP). The two key steps of the overall process are the accurate patterning of a poly(phthalaldehyde) resist layer of only 3.5 nm thickness, and the subsequent oxygen-plasma functionalization of an underlying neutral poly(styrene-random-methyl methacrylate) brush layer. We demonstrate that this method allows one to obtain aligned line/space patterns of poly(styrene-block-methyl methacrylate) BCP of 18.5 and 11.7 nm half-pitch. Defect-free alignment has been demonstrated over areas of tens of square micrometres. The main advantages of t-SPL are the absence of proximity effects, which enables the realization of patterns with 10 nm resolution, and its compatibility with standard DSA methods. In the brush activation step by oxygen-plasma exposure, we observe swelling of the brush. This effect is discussed in terms of the chemical reactions occurring in the exposed areas. Our results show that t-SPL can be a suitable method for research activities in the field of DSA, in particular for low-pitch, high-χ BCP to achieve sub-10 nm line/space patterns.