The microstructure of composites has a direct effect on the macroscale mechanical properties, local-global responses, and damage evolution. Therefore, accurate depicting and modeling of the composite’s microstructure is of great importance. Micromechanical methods usually employ an idealized repeating unit cell (RUC) in order to capture the effective properties of the composite material. For a unidirectional composite, a square array or hexagonal array are typically used to represent the microstructure where the decision on which one to choose is guided by acquired images of the fiber assemblage. While the experimental results for the average stiffness and stress-strain response of composites can be predicted with high accuracy using these idealized RUCs, the strength-prediction of such composites is far a more challenging task. Towards this goal, this study presents an extensive inquiry of the microstructure of unidirectional composite that has been made using scanning-electron-microscopy (SEM) combined with optical methods for the IM7/977-3 carbon-epoxy material system. Crucial characteristic phenomena of the microstructure imperfections, such as out-of-plan waviness of the laminae, fiber distribution, and large inter-laminae/inter-laminar resin pockets, have been identified. In addition, modeling of the accurate microstructure taken out of SEM scan has been made using the parametric high-fidelity-generalized-method-of-cells (HFGMC) micromechanical model. Using the scanned microstructure of the composite enhanced stress concentration under transverse and shear loading, especially in the matrix region between two or more close fibers. These phenomena are shown to directly affect the damage evolution at the microscale as well as the strength of the entire composite.