The graphoepitaxial assembly of cylinder-forming block copolymers assembled into holes is investigated through theoretically informed coarse grained Monte Carlo simulations (TICG MC). The aim is to identify conditions leading to assembly of cylinders that span the entire thickness of the holes, thereby enabling applications in lithography. Three hole geometries are considered, including cylinders, elliptical cylinders, and capsule-shaped holes. Four distinct morphologies of cylinder forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) block copolymers are observed in cylinders and elliptical holes, including cylinders, spheres, partial cylinders, and wall-bound cylinders. Additional morphologies are observed in capsule-shaped holes. PMMA cylinders that extend through the entire hole are found with PMMA-wetting surfaces; a weak wetting condition is needed on the bottom of the hole and a strong wetting condition is necessary on the sides of the hole. Simulated are also used to explore the morphologies that arise when holes are overfilled, or when PMMA homopolymers are added in blends with copolymers. We find that overfilling can alter considerably the morphological behavior of copolymers in cylinders and, for blends; we find that when the homopolymer concentration is >10%, the range of conditions for formation of PMMA cylinders that extend through the entire hole is increased. In general, results from simulations (TICG) are shown to be comparable to those of self-consistent (SCFT) calculations, except for conditions where fluctuations become important. (c) 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015, 53, 430-441