Figure shows SEM images of the BCP film, F1, rinsed monolayer, M1, and stained monolayer, M1S, during the first round of DSA. F1 is highly defective; while there is some degree of alignment, there are also large grains of isotropic fingerprint patterns. It is hard to determine any degree of nanostructure in M1 due to the low contrast of the polymer monolayer. However, after staining with SIS, M1S, the nanostructure of the monolayer becomes more apparent. In M1S, we see an aligned nanostructure comprised of two lines followed by one line of dots. We hypothesize that the two lines are stained PG(B-r-C) domains that have been anchored to the oxidized sidewalls of the chemical guiding patterns and the line of dots are grafted PG(B-r-C) domains in the unguided region. The oxidized sidewalls should anchor a greater number of polymer chains than the non-preferential backfilled brush resulting in full lines after SIS staining while the unguided PG(B-r-C) domain results in only dots similar to what is observed on the unguided fingerprint patterns, Figure . While the oxidized sidewalls also uptake TMA during the SIS process, they do not possess the observed line edge roughness (i.e., wiggling) that is characteristic of a polymer pattern (see Supporting Information). Although the lines have a high degree of edge roughness, the isotropic fingerprint patterns in F1 are not replicated in M1S, and each line or line of dots is continuous throughout the micrograph. While the underlying mechanism that prevents defects from being replicated in the monolayers is not well understood, previous studies using homopolymer inks have observed similar phenomena. Figure shows SEM images of the BCP film, F2, rinsed monolayer, M2, and stained monolayer, M2S, during the second round of DSA. F2 shows well aligned DSA with no observable defects over large areas.