Using self-consistent-field theory and dissipative particle dynamics, we study the self-assembly of cylinder-forming copolymers near homogeneous surfaces and two patterned substrates (with hexagonal pattern and sparse rectangular pattern, SRP), having periodically distributed regions of different wettability. These patterned templates are demonstrated to provide an effective means to enhance the stability of vertically aligned cylindrical domains ('cylindrical brushes') in thin films. The template-guided control over ordering and orientation is strongly dependent on affinity between the minority domains and the pattern. For SRP, when two characteristic length scales are involved, doubling the pattern frequency is observed in the resulting array of microdomains. (C) 2010 Elsevier B.V. All rights reserved.