Eigenstrain offers a versatile generic framework for the description of inelastic deformation that acts as the source of residual stresses. Focused ion beam (FIB) milling used for nanoscale machining is accompanied by target material modification by ion beam damage having residual stress consequences that can be described in terms of eigenstrain. Due to the lack of direct means of experimental determination of residual stress or eigenstrain at the nanoscale we adopt a hybrid approach that consists of eigenstrain abstraction from molecular dynamics simulation, its application within a finite element simulation of a flexible silicon cantilever, and satisfactory comparison of the prediction with experimental observation. Directions for further enquiry are briefly discussed. ", keywords = Focused ion beam milling; Molecular dynamics; Eigenstrain; Residual stress, isbn = 0167-577X, doi=https://doi.org/10.1016/j.matlet.2016.08.111