Directed self-assembly (DSA) of block copolymers has attracted much interest for its use as a low-cost, high throughput patterning tool to supplement existing lithographic techniques, and especially for its ability to easily pattern vertical interconnect accesses (VIAs).1 Assembling multiple cylinders in a single template has obvious advantages for feature density increase. However, denser patterning comes at a cost, due to more abundant defect modes2 and increased susceptibility to placement errors due to thermal fluctuations. Linear arrays of cylinders have been shown in a simplified model to contain collective excitations, ultimately leading to unbounded positional variance away from their equilibrium locations in a manner analogous to a one-dimensional crystal.3 In order to reduce this positional uncertainty, we introduce chemically selective stripes on the substrate of the system. These chemoepitaxially patterned regions create an energetic preference for the equilibrium configuration of the system, pinning the VIAs in place. In this study, we use three-dimensional self-consistent field theory (SCFT) simulations and complex Langevin (CL) sampling to investigate the effects of thermal fluctuations on cylinder positions in linear arrays of VIAs with preferentially striped substrates. We interrogate the relationship between stripe interaction strength and positional variance, compare the magnitude of reduction with a Landau-Peierls analysis on a simplified system, and propose a predictive model for placement error in similarly chemo patterned systems. Since the cylinders are flexible, we propose a maximum system height for linear arrays with acceptably low placement error.