The behavior and response of ceramic matrix composites (CMCs), in particular silicon carbide fiber reinforced silicon carbide matrix (SiC/SiC), is affected by many factors such as variation of fiber volume fraction, residual stresses resulting from processing of the composites at high temperature, random microstructures, and the presence of matrix flaws (e.g., voids, pores, cracks etc.) as well as general material nonlinearity and heterogeneity that occurs randomly in a composite. Residual stresses arising from the phase change of constituents are evaluated in this paper and it is shown that they do influence composite strength and need to be properly accounted for. Additionally, the microstructures (location of fiber centers, coating thickness etc.) of advanced CMCs are usually disordered (or random) and fiber diameter and strength typically have a distribution. They rarely resemble the ordered fiber packing (square, rectangular, or hexagonal) that is generally assumed in micromechanics-based models with periodic boundary conditions for computational expediency. These issues raise the question of how should one model such systems effectively? Can an ordered hexagonal packed repeating unit cell (RUC) accurately represent the random microstructure behavior? How many fibers need to be included to enable accurate representation? Clearly, the number of fibers within an RUC must be limited to insure a balance between accuracy and efficiency. NASA’s in-house micromechanics-based code MAC/GMC provides a framework to analyze such RUCs for the overall composite behavior and the FEAMAC computer code provides linkage of MAC/GMC to the commercial FEA code, ABAQUS. The appropriate level of discretization of the RUC as well as the analysis method employed, i.e., Generalized Method of Cells (GMC) or High Fidelity Generalized Method of Cells (HFGMC), is investigated in this paper in the context of a unidirectional as well as a cross-ply laminated CMC. Results including effective composite properties, proportional limit stress (an important design parameter) and fatigue are shown utilizing both GMC as well as HFGMC. Finally, a few multiscale analyses are performed on smooth bar test coupons as well as test coupons with features such as open-hole and double notches using FEAMAC. Best practices and guidance are provided to take these phenomena into account and keep a proper balance between fidelity (accuracy) and efficiency. Following these guidelines can account for important physics of the problem and provide significant advantages when performing large multiscale composite structural analyses. Finally, to demonstrate the multiscale analysis framework, a CMC gas turbine engine vane structure is analyzed involving a progressive damage model.