Recently, Focused Ion Beam (FIB) instruments have begun be applied to organic materials such as polymers and biological systems. This provides a novel tool for sectioning biological samples for analysis, or microfabrication with environment friendly materials. The modeling of nano/micro scale geometry accurately sculptured by FIB milling is crucial for generating the milling plan and process control, and for computer simulation for prediction and visualization of the milled geometry. However, modeling of the ion milling process on compound materials, especially for high aspect ratio feature, is still difficult due to the complexity of target material, as well as multiple physical and chemical interactions involved. In this study, a comprehensive model of ion milling with organic targets is presented to address the challenges using a simulation based approach. This platform has also been validated by milling different features on water ice in a cryogenic environment, and the simulation and experiment results show great consistency. With the proliferation of nanotechnology to biomedical and biomaterial domains, the proposed approach is expected to be a flexible tool for various applications involving novel and heterogeneous milling targets.