In an effort to reproduce computationally the observed evolution of microstructurally small fatigue cracks (MSFCs), a method is presented for generating conformal, finite‐element (FE), volume meshes from 3D measurements of MSFC propagation. The resulting volume meshes contain traction‐free surfaces that conform to incrementally measured 3D crack shapes. Grain morphologies measured using near‐field high‐energy X‐ray diffraction microscopy are also represented within the FE volume meshes. Proof‐of‐concept simulations are performed to demonstrate the utility of the mesh‐generation method. The proof‐of‐concept simulations employ a crystal‐plasticity constitutive model and are performed using the conformal FE meshes corresponding to successive crack‐growth increments. Although the simulations for each crack increment are currently independent of one another, they need not be, and transfer of material‐state information among successive crack‐increment meshes is discussed. The mesh‐generation method was developed using post‐mortem measurements, yet it is general enough that it can be applied to in‐situ measurements of 3D MSFC propagation.