Enabling extreme ultraviolet lithography (EUVL) as a viable and efficient sub-10 nm patterning tool requires addressing the critical issue of reducing line edge roughness (LER). Stochastic effects from random and local variability in photon distribution and photochemical reactions have been considered the primary cause of LER. However, polymer chain conformation has recently attracted attention as an additional factor influencing LER, necessitating detailed computational studies with explicit chain representation and photon distribution to overcome the existing approach based on continuum models and random variables. We developed a coarse-grained molecular simulation model for an EUV patterning process to investigate the effect of chain conformation variation and stochastic effects via photon shot noise and acid diffusion on the roughness of the pattern. Our molecular simulation demonstrated that final LER is most sensitive to the variation in photon distributions, while material distributions and acid diffusion rate also impact LER; thus, the intrinsic limit of LER is expected even at extremely suppressed stochastic effects. Furthermore, we proposed and tested a novel approach to improve the roughness by controlling the initial polymer chain orientation.