We have studied functionalization of guide pattern with brush treatment. Especially, the effect of brush treatment on ordering of nanodots formed on the guide pattern was investigated. We used polydimethylsiloxane (PDMS) as brush modification to form self-assembled nanodots on the guide pattern using polystyrene (PS) - PDMS as block copolymer. The brush treatment using toluene solvent made guide patterns of the electron beam (EB) drawn resist behave like PDMS guide patterns and good ordering of the nanodots has been achieved. It was demonstrated that the brush treatment enabled the PDMS nanodots to be regularly located in the desired positions defined by the EB drawn guide patterns.