Microscale residual stress may develop during the manufacturing of Carbon Fiber-Reinforced Polymer (CFRP) composites and negatively affect apparent macroscale mechanical properties. Accordingly, accurately capturing residual stress may be essential in computational methods used for composite material design. This work presents a new data-driven methodology for the evaluation of microscale residual stress in CFRPs using fiber push-out experiments with in situ scanning electron microscopy (SEM) imaging. SEM images reveal significant through-thickness matrix sink-in deformation in resin-rich areas after nearby fibers are pushed out, which is attributed to the release of microscale process-induced residual stress. The sink-in deformation is measured experimentally, and a Finite Element Model Updating (FEMU) method is used to retrieve the associated residual stress. The finite element (FE) analysis includes simulation of the curing process, test sample machining, and fiber push-out experiment. Significant out-of-plane matrix deformation larger than 1% of the specimen thickness is reported and associated with a high level of residual stress in resin-rich areas. This work emphasizes the importance of in situ data-driven characterization for integrated computational materials engineering (ICME) and material design.