In this work we present a first attempt to quantify the effect of flow deformation on the microstructure of semicrystalline polymers. This necessitates bridging the macroscopic flow length scale with the microscopic (segment) length scale of the semicrystalline structure. To achieve this connection we developed a hierarchical approach where a thermodynamically consistent macroscopic constitutive equation is interfaced with a microscopic lattice-based Monte Carlo (MC) simulation of the polymer chain conformation. We first illustrate this approach in a two-dimensional (21)) "toy" application where the 2D equivalent of a macroscopic constitutive equation based on reptation theory is applied to describe the chain deformation and extended free energy in the amorphous bulk phase. The values for the derivative of the free energy with respect to the mean segment orientation tensor, calculated for a planar extensional flow, are then used as an extended nonequilibrium. thermodynamic forcing term. This is added in a traditional Metropolis Monte Carlo scheme, developed for a 2D lattice representation of a lamellar semicrystalline polymer, to drive the flow-induced microstructure. Significant flow-induced changes are calculated, steadily increasing as the Weissenberg number increases. We subsequently extend these ideas further in a much more realistic three-dimensional (3D) application where the information for the thermodynamics of the bulk amorphous phase under a uniaxial extensional flow is extracted from a macroscopic network model, such as that of Phan-Thien and Tanner (PTT), connecting the free energy to the second moment of the end-to-end distance of a multisegment chain. Through a series of 3D nonequilibrium Monte Carlo simulations of both the amorphous and the semicrystalline microscopic morphologies, it is shown that the interaction of the flow-induced deformation with the semicrystalline microstructure is nonlinear: the amorphous interlamellar structure changes significantly from its corresponding homogeneous bulk amorphous state, even far away from the crystalline interface. Our approach allows for a quantitative estimation of this effect on both thermodynamic quantities, like the extended microscopic free energy, as well as various statistics of the chain conformations. (C) 2004 Elsevier B.V. All rights reserved.