We report the induction of perpendicularly oriented cylindrical domains in PS-b-PMMA block copolymer (BCP) films thicker than 100 nm by thermally annealing oil a substrate modified with it random copolymer. The effects of annealing temperature, composition of the substrate-modifying random copolymer, and BCP film thickness on the morphology of PMMA cylinder forming PS-b-PMMA were Studied. For BCP films thicker than 100 nm, the fabrication of perpendicular PMMA cylinders is highly dependent on both the substrate-modifying random copolymer and the annealing temperature as these two parameters control the interactions of the BCP with the substrate and the free surface, respectively, We found the best perpendicular structures to be created by using it random copolymer brush with a styrene fraction (P's,) near 0.70 and an annealing temperature near 230 degrees C. Perpendicular cylinder structures were achieved in similar to 300 nm thick Films using these conditions. When the BCP film was thicker than 300 rim, nucleation and growth of the microdomains proceeded independently from each interface. We present scanning electron microscope (SEM) and cross-sectional transmission electron microscope (TEM) images of these perpendicular Structures and explain the results oil the basis of previous simulation reports.